rs6624543

Variant names:

• chrX-71194792-C-G
• rs6624543
• ENST00000450860.1:n.267+3117G>C

Your query was ambiguous. Multiple possible variants found:

• chrX-71194792-C-G
• chrX-71194792-C-T

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.267+3117G>C variant causes a intron 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: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 1 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.285+3117G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000450860.1	n.267+3117G>C		intron_variant	Intron 1 of 1	3
ENSG00000228427	ENST00000652147.3	n.357+3117G>C		intron_variant	Intron 1 of 1
ENSG00000228427	ENST00000664514.4	n.599+3117G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 47938 AN: 108548 Hom.: 8593 Cov.: 21

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

African (AFR) AF: 0.636 AC: 18870 AN: 29689

American (AMR) AF: 0.333 AC: 3367 AN: 10112

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1501 AN: 2619

East Asian (EAS) AF: 0.506 AC: 1737 AN: 3434

South Asian (SAS) AF: 0.451 AC: 1152 AN: 2552

European-Finnish (FIN) AF: 0.302 AC: 1663 AN: 5498

Middle Eastern (MID) AF: 0.578 AC: 122 AN: 211

European-Non Finnish (NFE) AF: 0.354 AC: 18541 AN: 52348

Other (OTH) AF: 0.477 AC: 706 AN: 1481

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6624543; hg19: chrX-70414642;