rs6624543

chrX-71194792-C-GchrX-71194792-C-T

Variant summary

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

The ENST00000664514.3(ENSG00000228427):n.331+3117G>C 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 0.442 in 108,600 control chromosomes in the GnomAD database, including 8,602 homozygotes. There are 13,074 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 0.44 (8602 hom., 13074 hem., cov: 21)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985688	XR_001755878.2	n.285+3117G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664514.3	n.331+3117G>C		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.267+3117G>C		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.321+3117G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.442 AC: 47938 AN: 108548 Hom.: 8593 Cov.: 21 AF XY: 0.422 AC XY: 13041 AN XY: 30934

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.565

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.442 AC: 47980 AN: 108600 Hom.: 8602 Cov.: 21 AF XY: 0.422 AC XY: 13074 AN XY: 30996

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.477

Alfa AF: 0.409 Hom.: 2820

Bravo AF: 0.455

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6624543; hg19: chrX-70414642;