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. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.884 AC: 36705 AN: 41526

American (AMR) AF: 0.759 AC: 11599 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2733 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3379 AN: 5170

South Asian (SAS) AF: 0.893 AC: 4308 AN: 4822

European-Finnish (FIN) AF: 0.927 AC: 9822 AN: 10596

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58628 AN: 68004

Other (OTH) AF: 0.831 AC: 1756 AN: 2112

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6560812; hg19: chr10-2373105;