rs1349916

Variant names:

• chrX-122626457-A-G
• rs1349916

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 0.123 in 111,632 control chromosomes in the GnomAD database, including 682 homozygotes. There are 3,923 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 0.12 (682 hom., 3923 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 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: 0.123 AC: 13722 AN: 111577 Hom.: 683 Cov.: 23

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.0976

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.123 AC: 13729 AN: 111632 Hom.: 682 Cov.: 23 AF XY: 0.116 AC XY: 3923 AN XY: 33876

African (AFR) AF: 0.180 AC: 5505 AN: 30655

American (AMR) AF: 0.0977 AC: 1028 AN: 10524

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 361 AN: 2651

East Asian (EAS) AF: 0.138 AC: 480 AN: 3484

South Asian (SAS) AF: 0.136 AC: 370 AN: 2718

European-Finnish (FIN) AF: 0.0849 AC: 520 AN: 6126

Middle Eastern (MID) AF: 0.102 AC: 22 AN: 215

European-Non Finnish (NFE) AF: 0.0969 AC: 5139 AN: 53060

Other (OTH) AF: 0.111 AC: 168 AN: 1517

Alfa AF: 0.108 Hom.: 9420

Bravo AF: 0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.89
DANN	Benign	0.60
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1349916; hg19: chrX-121760310;