rs1505695

Positions:

• chr2-6800086-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.359

Alfa AF: 0.332 Hom.: 1253

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1505695; hg19: chr2-6940217;