6-147986782-A-G

Variant names:

• chr6-147986782-A-G
• rs6570808
• ENST00000773311.1:n.49-31996A>G

Variant summary

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

The ENST00000773311.1(ENSG00000287976):​n.49-31996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,218 control chromosomes in the GnomAD database, including 65,633 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 0.93 (65633 hom., cov: 32)
• Consequence: ENSG00000287976 ENST00000773311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 4 publications found

Genes affected

ENSG00000287976 (HGNC:):

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 = 0.941 is higher than 0.05.

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
ENSG00000287976	ENST00000773311.1	n.49-31996A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141111 AN: 152100 Hom.: 65577 Cov.: 32

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.928 AC: 141224 AN: 152218 Hom.: 65633 Cov.: 32 AF XY: 0.926 AC XY: 68904 AN XY: 74416

African (AFR) AF: 0.928 AC: 38559 AN: 41546

American (AMR) AF: 0.843 AC: 12883 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3170 AN: 3468

East Asian (EAS) AF: 0.884 AC: 4565 AN: 5164

South Asian (SAS) AF: 0.912 AC: 4394 AN: 4818

European-Finnish (FIN) AF: 0.958 AC: 10156 AN: 10600

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64404 AN: 68022

Other (OTH) AF: 0.921 AC: 1948 AN: 2114

Alfa AF: 0.931 Hom.: 109475

Bravo AF: 0.916

Asia WGS AF: 0.911 AC: 3171 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	0.27
DANN	Benign	0.54
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs6570808; hg19: chr6-148307918;