X-71193185-T-C

Position:

• chrX-71193185-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664514.3(ENSG00000228427):​n.331+4724A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 110,052 control chromosomes in the GnomAD database, including 10,262 homozygotes. There are 15,807 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 0.49 (10262 hom., 15807 hem., cov: 22)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985688	XR_001755878.2	n.285+4724A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664514.3	n.331+4724A>G		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.267+4724A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.321+4724A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.493 AC: 54241 AN: 109998 Hom.: 10254 Cov.: 22 AF XY: 0.489 AC XY: 15762 AN XY: 32254

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.493 AC: 54295 AN: 110052 Hom.: 10262 Cov.: 22 AF XY: 0.489 AC XY: 15807 AN XY: 32318

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.543

Alfa AF: 0.445 Hom.: 3128

Bravo AF: 0.518

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6624542; hg19: chrX-70413035;