rs6638724

Variant names:

• chrX-4388674-G-A
• rs6638724
• ENST00000729249.1:n.338-2570G>A

Variant summary

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

The ENST00000729249.1(ENSG00000295325):​n.338-2570G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 108,729 control chromosomes in the GnomAD database, including 3,178 homozygotes. There are 4,785 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 0.17 (3178 hom., 4785 hem., cov: 21)
• Consequence: ENSG00000295325 ENST00000729249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729249.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295325	ENST00000729249.1		n.338-2570G>A		intron	N/A
	ENSG00000295325	ENST00000729250.1		n.170-2570G>A		intron	N/A
	ENSG00000295325	ENST00000729251.1		n.199-2570G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 18287 AN: 108686 Hom.: 3173 Cov.: 21

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.00991

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0515

Gnomad NFE AF: 0.00505

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.169 AC: 18339 AN: 108729 Hom.: 3178 Cov.: 21 AF XY: 0.153 AC XY: 4785 AN XY: 31225

African (AFR) AF: 0.506 AC: 14947 AN: 29522

American (AMR) AF: 0.115 AC: 1166 AN: 10146

Ashkenazi Jewish (ASJ) AF: 0.00991 AC: 26 AN: 2623

East Asian (EAS) AF: 0.367 AC: 1228 AN: 3349

South Asian (SAS) AF: 0.135 AC: 337 AN: 2492

European-Finnish (FIN) AF: 0.0261 AC: 146 AN: 5590

Middle Eastern (MID) AF: 0.0429 AC: 9 AN: 210

European-Non Finnish (NFE) AF: 0.00505 AC: 266 AN: 52640

Other (OTH) AF: 0.145 AC: 214 AN: 1479

Alfa AF: 0.108 Hom.: 754

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.29
PhyloP100		-0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6638724;

hg19: chrX-4306715;

COSMIC: COSV54750748;