6-112101444-T-C

Variant names:

• chr6-112101444-T-C
• rs2010315
• NM_001033564.3:c.*657T>C

Variant summary

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

The NM_001033564.3(FAM229B):​c.*657T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,178 control chromosomes in the GnomAD database, including 7,149 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 0.30 (7149 hom., cov: 33)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: FAM229B NM_001033564.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 6 publications found

Genes affected

FAM229B (HGNC:33858): (family with sequence similarity 229 member B)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033564.3. 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
	FAM229B	NM_001033564.3	MANE Select	c.*657T>C		3_prime_UTR	Exon 4 of 4	NP_001028736.1	Q4G0N7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM229B	ENST00000368656.7	TSL:1 MANE Select	c.*657T>C		3_prime_UTR	Exon 4 of 4	ENSP00000357645.2	Q4G0N7
	FAM229B	ENST00000856566.1		c.*657T>C		3_prime_UTR	Exon 4 of 4	ENSP00000526625.1
	FAM229B	ENST00000932582.1		c.*657T>C		3_prime_UTR	Exon 2 of 2	ENSP00000602641.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45347 AN: 152054 Hom.: 7136 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.298 AC: 45404 AN: 152172 Hom.: 7149 Cov.: 33 AF XY: 0.291 AC XY: 21683 AN XY: 74404

African (AFR) AF: 0.410 AC: 17000 AN: 41506

American (AMR) AF: 0.226 AC: 3452 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1657 AN: 5168

South Asian (SAS) AF: 0.159 AC: 765 AN: 4824

European-Finnish (FIN) AF: 0.206 AC: 2185 AN: 10606

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18369 AN: 67984

Other (OTH) AF: 0.303 AC: 640 AN: 2114

Alfa AF: 0.285 Hom.: 1326

Bravo AF: 0.308

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.24
PhyloP100		-1.6
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: rs2010315; hg19: chr6-112422647;