rs6806731

Variant names:

• chr3-104416411-G-A
• rs6806731
• ENST00000749799.1:n.275-21284C>T

Variant summary

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

The ENST00000749799.1(ENSG00000297654):​n.275-21284C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,022 control chromosomes in the GnomAD database, including 39,635 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 0.72 (39635 hom., cov: 31)
• Consequence: ENSG00000297654 ENST00000749799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 2 publications found

Genes affected

ENSG00000297654 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000749799.1. 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
	ENSG00000297654	ENST00000749799.1		n.275-21284C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108977 AN: 151904 Hom.: 39607 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.717 AC: 109045 AN: 152022 Hom.: 39635 Cov.: 31 AF XY: 0.720 AC XY: 53480 AN XY: 74306

African (AFR) AF: 0.608 AC: 25186 AN: 41438

American (AMR) AF: 0.759 AC: 11595 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3470

East Asian (EAS) AF: 0.671 AC: 3460 AN: 5160

South Asian (SAS) AF: 0.767 AC: 3707 AN: 4832

European-Finnish (FIN) AF: 0.806 AC: 8521 AN: 10578

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.764 AC: 51947 AN: 67960

Other (OTH) AF: 0.708 AC: 1496 AN: 2112

Alfa AF: 0.741 Hom.: 121045

Bravo AF: 0.706

Asia WGS AF: 0.728 AC: 2520 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.055
DANN	Benign	0.38
PhyloP100		-0.84

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6806731;

hg19: chr3-104135255;

COSMIC: COSV56464222;