6-140979939-A-G

Variant names:

• chr6-140979939-A-G
• rs1856363
• ENST00000765626.1:n.236+37976A>G

Variant summary

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

The ENST00000765626.1(ENSG00000299692):​n.236+37976A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 151,840 control chromosomes in the GnomAD database, including 35,968 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 0.68 (35968 hom., cov: 31)
• Consequence: ENSG00000299692 ENST00000765626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 1 publications found

Genes affected

ENSG00000299692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765626.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299692	ENST00000765626.1		n.236+37976A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103683 AN: 151722 Hom.: 35943 Cov.: 31

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.683 AC: 103744 AN: 151840 Hom.: 35968 Cov.: 31 AF XY: 0.674 AC XY: 50020 AN XY: 74194

African (AFR) AF: 0.776 AC: 32136 AN: 41392

American (AMR) AF: 0.614 AC: 9345 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3466

East Asian (EAS) AF: 0.404 AC: 2074 AN: 5132

South Asian (SAS) AF: 0.510 AC: 2462 AN: 4824

European-Finnish (FIN) AF: 0.636 AC: 6724 AN: 10578

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46718 AN: 67912

Other (OTH) AF: 0.688 AC: 1452 AN: 2110

Alfa AF: 0.677 Hom.: 17881

Bravo AF: 0.687

Asia WGS AF: 0.505 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.69
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1856363; hg19: chr6-141301076; COSMIC: COSV60288788;