chr10-6008329-G-A

Variant names:

• chr10-6008329-G-A
• rs11256313

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 0.111 in 152,072 control chromosomes in the GnomAD database, including 1,077 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 0.11 (1077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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: 0.110 AC: 16790 AN: 151954 Hom.: 1071 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0977

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.111 AC: 16822 AN: 152072 Hom.: 1077 Cov.: 32 AF XY: 0.113 AC XY: 8412 AN XY: 74322

African (AFR) AF: 0.103 AC: 4265 AN: 41470

American (AMR) AF: 0.143 AC: 2185 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1219 AN: 5166

South Asian (SAS) AF: 0.118 AC: 571 AN: 4820

European-Finnish (FIN) AF: 0.124 AC: 1306 AN: 10558

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0977 AC: 6640 AN: 67980

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.106 Hom.: 109

Bravo AF: 0.109

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.73
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs11256313; hg19: chr10-6050292; COSMIC: COSV56920084;