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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374020	XR_924301.3	n.165+40099C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297654	ENST00000749799.1	n.275-21284C>T		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs6806731; hg19: chr3-104135255; COSMIC: COSV56464222;