rs679582

Variant names:

• chr6-139510043-G-A
• rs679582
• ENST00000647815.1:n.134+23428G>A

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+23428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,954 control chromosomes in the GnomAD database, including 24,406 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 0.56 (24406 hom., cov: 32)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 7 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647815.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226571	ENST00000647815.1		n.134+23428G>A		intron	N/A
	ENSG00000226571	ENST00000775574.1		n.194-37199G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84984 AN: 151836 Hom.: 24384 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.560 AC: 85053 AN: 151954 Hom.: 24406 Cov.: 32 AF XY: 0.560 AC XY: 41563 AN XY: 74280

African (AFR) AF: 0.453 AC: 18763 AN: 41432

American (AMR) AF: 0.582 AC: 8874 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2290 AN: 3466

East Asian (EAS) AF: 0.307 AC: 1586 AN: 5158

South Asian (SAS) AF: 0.713 AC: 3434 AN: 4818

European-Finnish (FIN) AF: 0.547 AC: 5769 AN: 10554

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42356 AN: 67958

Other (OTH) AF: 0.578 AC: 1218 AN: 2106

Alfa AF: 0.588 Hom.: 39648

Bravo AF: 0.552

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.72
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs679582; hg19: chr6-139831180; COSMIC: COSV69428605;