rs11796357

Variant names:

• chrX-69578860-A-G
• rs11796357

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 0.161 in 110,197 control chromosomes in the GnomAD database, including 1,401 homozygotes. There are 4,994 hemizygotes in GnomAD. 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 0.16 (1401 hom., 4994 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.161 AC: 17755 AN: 110137 Hom.: 1401 Cov.: 21

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0134

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.161 AC: 17752 AN: 110197 Hom.: 1401 Cov.: 21 AF XY: 0.154 AC XY: 4994 AN XY: 32451

African (AFR) AF: 0.0329 AC: 1003 AN: 30459

American (AMR) AF: 0.149 AC: 1541 AN: 10327

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 528 AN: 2626

East Asian (EAS) AF: 0.0135 AC: 47 AN: 3490

South Asian (SAS) AF: 0.163 AC: 416 AN: 2554

European-Finnish (FIN) AF: 0.237 AC: 1360 AN: 5730

Middle Eastern (MID) AF: 0.119 AC: 25 AN: 210

European-Non Finnish (NFE) AF: 0.237 AC: 12446 AN: 52623

Other (OTH) AF: 0.135 AC: 204 AN: 1507

Alfa AF: 0.205 Hom.: 6020

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.25
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs11796357; hg19: chrX-68798703; COSMIC: COSV69029602;