rs61742285

Variant names:

• chr4-17639257-C-G
• rs61742285
• NM_015688.2:c.2659G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-17639257-C-G
• chr4-17639257-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_015688.2(FAM184B):​c.2659G>C​(p.Glu887Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0224 in 1,551,624 control chromosomes in the GnomAD database, including 500 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.015 (29 hom., cov: 32)
  • Exomes 𝑓: 0.023 (471 hom.)
• Consequence: FAM184B NM_015688.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.32
• Publications: 7 publications found

Genes affected

FAM184B (HGNC:29235): (family with sequence similarity 184 member B)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0059881806).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0152 (2313/152326) while in subpopulation NFE AF = 0.0253 (1722/68026). AF 95% confidence interval is 0.0243. There are 29 homozygotes in GnomAd4. There are 1026 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 29 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015688.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM184B	NM_015688.2	MANE Select	c.2659G>C	p.Glu887Gln	missense	Exon 14 of 18	NP_056503.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM184B	ENST00000265018.4	TSL:1 MANE Select	c.2659G>C	p.Glu887Gln	missense	Exon 14 of 18	ENSP00000265018.3
	FAM184B	ENST00000954035.1		c.2548G>C	p.Glu850Gln	missense	Exon 13 of 17	ENSP00000624094.1

Frequencies

GnomAD3 genomes AF: 0.0152 AC: 2312 AN: 152208 Hom.: 29 Cov.: 32

Gnomad AFR AF: 0.00480

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.00917

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0253

Gnomad OTH AF: 0.0124

GnomAD2 exomes AF: 0.0134 AC: 2081 AN: 155872 AF XY: 0.0135

Gnomad AFR exome AF: 0.00356

Gnomad AMR exome AF: 0.00664

Gnomad ASJ exome AF: 0.0134

Gnomad EAS exome AF: 0.0000918

Gnomad FIN exome AF: 0.0107

Gnomad NFE exome AF: 0.0241

Gnomad OTH exome AF: 0.0146

GnomAD4 exome AF: 0.0232 AC: 32497 AN: 1399298 Hom.: 471 Cov.: 34 AF XY: 0.0225 AC XY: 15547 AN XY: 690156

African (AFR) AF: 0.00304 AC: 96 AN: 31590

American (AMR) AF: 0.00667 AC: 238 AN: 35702

Ashkenazi Jewish (ASJ) AF: 0.0131 AC: 331 AN: 25178

East Asian (EAS) AF: 0.0000839 AC: 3 AN: 35738

South Asian (SAS) AF: 0.00380 AC: 301 AN: 79234

European-Finnish (FIN) AF: 0.0123 AC: 605 AN: 49222

Middle Eastern (MID) AF: 0.00386 AC: 22 AN: 5698

European-Non Finnish (NFE) AF: 0.0278 AC: 29948 AN: 1078942

Other (OTH) AF: 0.0164 AC: 953 AN: 57994

GnomAD4 genome AF: 0.0152 AC: 2313 AN: 152326 Hom.: 29 Cov.: 32 AF XY: 0.0138 AC XY: 1026 AN XY: 74488

African (AFR) AF: 0.00479 AC: 199 AN: 41582

American (AMR) AF: 0.00916 AC: 140 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00331 AC: 16 AN: 4830

European-Finnish (FIN) AF: 0.0105 AC: 112 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0253 AC: 1722 AN: 68026

Other (OTH) AF: 0.0123 AC: 26 AN: 2114

Alfa AF: 0.0221 Hom.: 41

Bravo AF: 0.0146

TwinsUK AF: 0.0254 AC: 94

ALSPAC AF: 0.0298 AC: 115

ESP6500AA AF: 0.00361 AC: 5

ESP6500EA AF: 0.0264 AC: 84

ExAC AF: 0.00971 AC: 249

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.45	T
BayesDel_noAF	Benign	-0.38
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.080	T
Eigen	Uncertain	0.37
Eigen_PC	Uncertain	0.40
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.78	T
MetaRNN	Benign	0.0060	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	L
PhyloP100		5.3
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	-0.34	N
REVEL	Benign	0.20
Sift	Benign	0.72	T
Sift4G	Uncertain	0.030	D
Polyphen		1.0	D
Vest4		0.47
ClinPred		0.014	T
GERP RS		5.0
Varity_R		0.22
gMVP		0.18
Mutation Taster		=94/6	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs61742285; hg19: chr4-17640880;