rs5967638

Variant names:

• chrX-85840734-G-A
• rs5967638

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 0.153 in 112,512 control chromosomes in the GnomAD database, including 1,762 homozygotes. There are 4,974 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 0.15 (1762 hom., 4974 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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: 0.153 AC: 17155 AN: 112462 Hom.: 1761 Cov.: 23

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.0940

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.153 AC: 17193 AN: 112512 Hom.: 1762 Cov.: 23 AF XY: 0.143 AC XY: 4974 AN XY: 34708

African (AFR) AF: 0.367 AC: 11338 AN: 30868

American (AMR) AF: 0.0876 AC: 939 AN: 10723

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 313 AN: 2652

East Asian (EAS) AF: 0.260 AC: 918 AN: 3533

South Asian (SAS) AF: 0.0781 AC: 214 AN: 2739

European-Finnish (FIN) AF: 0.0160 AC: 100 AN: 6263

Middle Eastern (MID) AF: 0.134 AC: 29 AN: 216

European-Non Finnish (NFE) AF: 0.0567 AC: 3022 AN: 53297

Other (OTH) AF: 0.166 AC: 256 AN: 1540

Alfa AF: 0.0963 Hom.: 2855

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.83
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs5967638; hg19: chrX-85095739;