rs6625761

Positions:

• chrX-71191723-G-A

Variant summary

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

The ENST00000664514.3(ENSG00000228427):​n.331+6186C>T 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 0.485 in 110,203 control chromosomes in the GnomAD database, including 9,726 homozygotes. There are 15,797 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 (9726 hom., 15797 hem., cov: 22)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985688	XR_001755878.2	n.285+6186C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664514.3	n.331+6186C>T		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.267+6186C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.321+6186C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 53422 AN: 110151 Hom.: 9719 Cov.: 22 AF XY: 0.486 AC XY: 15759 AN XY: 32447

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.485 AC: 53467 AN: 110203 Hom.: 9726 Cov.: 22 AF XY: 0.486 AC XY: 15797 AN XY: 32509

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.537

Alfa AF: 0.440 Hom.: 3077

Bravo AF: 0.507

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6625761; hg19: chrX-70411573;