rs6733795

Variant names:

• chr2-85333360-G-A
• rs6733795
• ENST00000825767.1:n.210+6538G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-85333360-G-A
• chr2-85333360-G-C
• chr2-85333360-G-T

Variant summary

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

The ENST00000825767.1(ENSG00000307411):​n.210+6538G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 150,156 control chromosomes in the GnomAD database, including 25,208 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 0.57 (25208 hom., cov: 33)
• Consequence: ENSG00000307411 ENST00000825767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 4 publications found

Genes affected

ENSG00000307411 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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
ENSG00000307411	ENST00000825767.1	n.210+6538G>A		intron_variant	Intron 1 of 1
ENSG00000307411	ENST00000825768.1	n.195+6538G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.573 AC: 85964 AN: 150050 Hom.: 25187 Cov.: 33

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.573 AC: 86011 AN: 150156 Hom.: 25208 Cov.: 33 AF XY: 0.583 AC XY: 42780 AN XY: 73432

African (AFR) AF: 0.450 AC: 17836 AN: 39602

American (AMR) AF: 0.704 AC: 10723 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2265 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4595 AN: 5182

South Asian (SAS) AF: 0.712 AC: 3434 AN: 4822

European-Finnish (FIN) AF: 0.593 AC: 6273 AN: 10576

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38835 AN: 67968

Other (OTH) AF: 0.629 AC: 1315 AN: 2092

Alfa AF: 0.566 Hom.: 6559

Bravo AF: 0.568

Asia WGS AF: 0.788 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs6733795; hg19: chr2-85560483;