rs2315065

Variant names:

• chr6-160687112-C-A
• rs2315065

Your query was ambiguous. Multiple possible variants found:

• chr6-160687112-C-A
• chr6-160687112-C-T

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 0.0546 in 152,248 control chromosomes in the GnomAD database, including 346 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 0.055 (346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.088 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: 0.0547 AC: 8324 AN: 152130 Hom.: 346 Cov.: 32

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0312

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0546 AC: 8320 AN: 152248 Hom.: 346 Cov.: 32 AF XY: 0.0505 AC XY: 3756 AN XY: 74442

African (AFR) AF: 0.0160 AC: 666 AN: 41554

American (AMR) AF: 0.0469 AC: 717 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0312 AC: 108 AN: 3464

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.00891 AC: 43 AN: 4824

European-Finnish (FIN) AF: 0.0509 AC: 540 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0899 AC: 6112 AN: 68010

Other (OTH) AF: 0.0493 AC: 104 AN: 2110

Alfa AF: 0.0563 Hom.: 185

Bravo AF: 0.0526

Asia WGS AF: 0.00693 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0090
DANN	Benign	0.49
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2315065; hg19: chr6-161108144; COSMIC: COSV69432095;