rs6560812

Variant names:

• chr10-2330911-A-C
• rs6560812

Your query was ambiguous. Multiple possible variants found:

• chr10-2330911-A-C
• chr10-2330911-A-T

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 0.854 in 152,194 control chromosomes in the GnomAD database, including 55,868 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 0.85 (55868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.876 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: 0.854 AC: 129919 AN: 152076 Hom.: 55835 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.854 AC: 130008 AN: 152194 Hom.: 55868 Cov.: 32 AF XY: 0.855 AC XY: 63603 AN XY: 74396

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.893

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.831

Alfa AF: 0.855 Hom.: 11315

Bravo AF: 0.840

Asia WGS AF: 0.775 AC: 2697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6560812; hg19: chr10-2373105;