rs6639932

Variant names:

• chrX-4388236-A-G
• rs6639932
• ENST00000729249.1:n.338-3008A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000729249.1(ENSG00000295325):​n.338-3008A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 110,366 control chromosomes in the GnomAD database, including 1,180 homozygotes. There are 3,179 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 0.10 (1180 hom., 3179 hem., cov: 22)
• Consequence: ENSG00000295325 ENST00000729249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 0 publications found

Genes affected

ENSG00000295325 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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
ENSG00000295325	ENST00000729249.1	n.338-3008A>G		intron_variant	Intron 2 of 2
ENSG00000295325	ENST00000729250.1	n.170-3008A>G		intron_variant	Intron 1 of 1
ENSG00000295325	ENST00000729251.1	n.199-3008A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 11514 AN: 110320 Hom.: 1174 Cov.: 22

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0339

Gnomad NFE AF: 0.00415

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.105 AC: 11547 AN: 110366 Hom.: 1180 Cov.: 22 AF XY: 0.0974 AC XY: 3179 AN XY: 32642

African (AFR) AF: 0.283 AC: 8536 AN: 30175

American (AMR) AF: 0.0853 AC: 881 AN: 10331

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 29 AN: 2629

East Asian (EAS) AF: 0.360 AC: 1238 AN: 3437

South Asian (SAS) AF: 0.136 AC: 339 AN: 2486

European-Finnish (FIN) AF: 0.0273 AC: 162 AN: 5930

Middle Eastern (MID) AF: 0.0278 AC: 6 AN: 216

European-Non Finnish (NFE) AF: 0.00415 AC: 220 AN: 52970

Other (OTH) AF: 0.0900 AC: 136 AN: 1511

Alfa AF: 0.0667 Hom.: 368

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.9
DANN	Benign	0.49
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs6639932; hg19: chrX-4306277;