chr4-17735633-T-C

Variant names:

• chr4-17735633-T-C
• rs13104297
• NM_015688.2:c.142-25989A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015688.2(FAM184B):​c.142-25989A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 150,582 control chromosomes in the GnomAD database, including 6,118 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 0.28 (6118 hom., cov: 31)
• Consequence: FAM184B NM_015688.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 1 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 (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM184B	NM_015688.2	c.142-25989A>G		intron_variant	Intron 1 of 17	ENST00000265018.4	NP_056503.1
FAM184B	XM_047450066.1	c.142-25989A>G		intron_variant	Intron 1 of 16		XP_047306022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM184B	ENST00000265018.4	c.142-25989A>G		intron_variant	Intron 1 of 17	1	NM_015688.2	ENSP00000265018.3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42164 AN: 150464 Hom.: 6117 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.303

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.280 AC: 42178 AN: 150582 Hom.: 6118 Cov.: 31 AF XY: 0.272 AC XY: 20054 AN XY: 73642

African (AFR) AF: 0.263 AC: 10552 AN: 40124

American (AMR) AF: 0.266 AC: 4036 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1311 AN: 3468

East Asian (EAS) AF: 0.131 AC: 678 AN: 5178

South Asian (SAS) AF: 0.309 AC: 1489 AN: 4816

European-Finnish (FIN) AF: 0.162 AC: 1717 AN: 10596

Middle Eastern (MID) AF: 0.303 AC: 88 AN: 290

European-Non Finnish (NFE) AF: 0.313 AC: 21280 AN: 67924

Other (OTH) AF: 0.301 AC: 631 AN: 2098

Alfa AF: 0.289 Hom.: 838

Bravo AF: 0.284

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.42
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

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: rs13104297; hg19: chr4-17737256;