rs2314852

Variant names:

• chr6-160701755-G-A
• rs2314852

Your query was ambiguous. Multiple possible variants found:

• chr6-160701755-G-A
• chr6-160701755-G-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 0.78 in 152,124 control chromosomes in the GnomAD database, including 47,333 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 0.78 (47333 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 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: 0.780 AC: 118523 AN: 152006 Hom.: 47285 Cov.: 31

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.780 AC: 118625 AN: 152124 Hom.: 47333 Cov.: 31 AF XY: 0.770 AC XY: 57233 AN XY: 74348

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.763

Alfa AF: 0.755 Hom.: 2371

Bravo AF: 0.769

Asia WGS AF: 0.531 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2314852; hg19: chr6-161122787; COSMIC: COSV51985910;