16-62547932-G-A

Variant names:

• chr16-62547932-G-A
• rs1077462
• ENST00000841257.1:n.103-22083G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000841257.1(ENSG00000309454):​n.103-22083G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0025 in 150,526 control chromosomes in the GnomAD database, including 1 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 0.0025 (1 hom., cov: 31)
• Consequence: ENSG00000309454 ENST00000841257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.29
• Publications: 2 publications found

Genes affected

ENSG00000309454 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309454	ENST00000841257.1	n.103-22083G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00251 AC: 377 AN: 150436 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00876

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000862

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000591

Gnomad OTH AF: 0.000968

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

GnomAD4 genome AF: 0.00250 AC: 377 AN: 150526 Hom.: 1 Cov.: 31 AF XY: 0.00230 AC XY: 169 AN XY: 73374

African (AFR) AF: 0.00874 AC: 358 AN: 40966

American (AMR) AF: 0.000861 AC: 13 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3460

East Asian (EAS) AF: 0.00 AC: 0 AN: 5018

South Asian (SAS) AF: 0.00 AC: 0 AN: 4758

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10266

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000591 AC: 4 AN: 67672

Other (OTH) AF: 0.000959 AC: 2 AN: 2086

Alfa AF: 0.00243 Hom.: 1

Bravo AF: 0.00279

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.012
DANN	Benign	0.64
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs1077462; hg19: chr16-62581836;