rs3131863

Variant names:

• chr6-29705706-G-A
• rs3131863
• ENST00000850325.1:n.220-2734G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29705706-G-A
• chr6-29705706-G-C
• chr6-29705706-G-T

Variant summary

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

The ENST00000850325.1(ENSG00000310484):​n.220-2734G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 152,092 control chromosomes in the GnomAD database, including 36,622 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 0.69 (36622 hom., cov: 33)
• Consequence: ENSG00000310484 ENST00000850325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 25 publications found

Genes affected

ENSG00000310484 (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 (AMR) allele frequency at 95% confidence interval = 0.704 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
ENSG00000310484	ENST00000850325.1	n.220-2734G>A		intron_variant	Intron 1 of 2
ENSG00000310484	ENST00000850326.1	n.202-2734G>A		intron_variant	Intron 1 of 1
ENSG00000310484	ENST00000850327.1	n.123-2734G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105245 AN: 151972 Hom.: 36589 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.693 AC: 105328 AN: 152092 Hom.: 36622 Cov.: 33 AF XY: 0.686 AC XY: 50976 AN XY: 74328

African (AFR) AF: 0.688 AC: 28554 AN: 41496

American (AMR) AF: 0.715 AC: 10934 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2470 AN: 3470

East Asian (EAS) AF: 0.690 AC: 3557 AN: 5158

South Asian (SAS) AF: 0.637 AC: 3069 AN: 4816

European-Finnish (FIN) AF: 0.585 AC: 6183 AN: 10562

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48244 AN: 67984

Other (OTH) AF: 0.706 AC: 1489 AN: 2110

Alfa AF: 0.711 Hom.: 90744

Bravo AF: 0.705

Asia WGS AF: 0.738 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs3131863; hg19: chr6-29673483;