rs1505695

Variant names:

• chr2-6800086-T-C
• rs1505695

Variant summary

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

The variant allele was found at a frequency of 0.323 in 152,076 control chromosomes in the GnomAD database, including 8,052 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 0.32 (8052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 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

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49038 AN: 151958 Hom.: 8045 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.323 AC: 49060 AN: 152076 Hom.: 8052 Cov.: 32 AF XY: 0.328 AC XY: 24408 AN XY: 74344

African (AFR) AF: 0.256 AC: 10612 AN: 41482

American (AMR) AF: 0.389 AC: 5946 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3470

East Asian (EAS) AF: 0.397 AC: 2053 AN: 5172

South Asian (SAS) AF: 0.337 AC: 1623 AN: 4822

European-Finnish (FIN) AF: 0.367 AC: 3873 AN: 10564

Middle Eastern (MID) AF: 0.400 AC: 116 AN: 290

European-Non Finnish (NFE) AF: 0.328 AC: 22289 AN: 67974

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.330 Hom.: 1282

Bravo AF: 0.320

Asia WGS AF: 0.372 AC: 1290 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs1505695; hg19: chr2-6940217;