rs11597367

Variant names:

• chr10-6065571-A-G
• rs11597367

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 0.201 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.0228

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.256

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11597367; hg19: chr10-6107534;