X-153440790-C-T

Variant names:

• chrX-153440790-C-T
• rs2980024

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 0.243 in 111,824 control chromosomes in the GnomAD database, including 3,192 homozygotes. There are 8,053 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 0.24 (3192 hom., 8053 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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: 0.243 AC: 27153 AN: 111768 Hom.: 3189 Cov.: 24

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.00450

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.243 AC: 27157 AN: 111824 Hom.: 3192 Cov.: 24 AF XY: 0.237 AC XY: 8053 AN XY: 34030

African (AFR) AF: 0.0497 AC: 1539 AN: 30972

American (AMR) AF: 0.214 AC: 2282 AN: 10640

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1040 AN: 2641

East Asian (EAS) AF: 0.00451 AC: 16 AN: 3549

South Asian (SAS) AF: 0.161 AC: 442 AN: 2739

European-Finnish (FIN) AF: 0.375 AC: 2235 AN: 5966

Middle Eastern (MID) AF: 0.335 AC: 72 AN: 215

European-Non Finnish (NFE) AF: 0.357 AC: 18884 AN: 52913

Other (OTH) AF: 0.266 AC: 404 AN: 1516

Alfa AF: 0.293 Hom.: 2361

Bravo AF: 0.226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2980024; hg19: chrX-152706248;