rs11597367

Variant names:

• chr10-6065571-A-G
• rs11597367

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 0.201 in 152,116 control chromosomes in the GnomAD database, including 3,667 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 0.20 (3667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.201 AC: 30579 AN: 151998 Hom.: 3665 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.201 AC: 30586 AN: 152116 Hom.: 3667 Cov.: 32 AF XY: 0.197 AC XY: 14626 AN XY: 74358

African (AFR) AF: 0.108 AC: 4476 AN: 41494

American (AMR) AF: 0.236 AC: 3607 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3468

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5184

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1787 AN: 10576

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17310 AN: 67998

Other (OTH) AF: 0.256 AC: 542 AN: 2114

Alfa AF: 0.226 Hom.: 525

Bravo AF: 0.201

Asia WGS AF: 0.142 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.16
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs11597367; hg19: chr10-6107534;