rs6540401

Variant names:

• chrX-148237293-C-A
• rs6540401
• ENST00000821191.1:n.687+15358C>A

Variant summary

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

The ENST00000821191.1(ENSG00000306798):​n.687+15358C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 110,217 control chromosomes in the GnomAD database, including 1,765 homozygotes. There are 4,473 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 0.15 (1765 hom., 4473 hem., cov: 22)
• Consequence: ENSG00000306798 ENST00000821191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 2 publications found

Genes affected

ENSG00000306798 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306798	ENST00000821191.1	n.687+15358C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 16851 AN: 110163 Hom.: 1764 Cov.: 22

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.00292

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.00171

Gnomad SAS AF: 0.0649

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.153 AC: 16872 AN: 110217 Hom.: 1765 Cov.: 22 AF XY: 0.137 AC XY: 4473 AN XY: 32537

African (AFR) AF: 0.365 AC: 10989 AN: 30089

American (AMR) AF: 0.0749 AC: 777 AN: 10368

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 227 AN: 2623

East Asian (EAS) AF: 0.00171 AC: 6 AN: 3505

South Asian (SAS) AF: 0.0635 AC: 158 AN: 2489

European-Finnish (FIN) AF: 0.0358 AC: 212 AN: 5925

Middle Eastern (MID) AF: 0.146 AC: 31 AN: 212

European-Non Finnish (NFE) AF: 0.0810 AC: 4279 AN: 52824

Other (OTH) AF: 0.128 AC: 191 AN: 1497

Alfa AF: 0.121 Hom.: 687

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.39
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6540401; hg19: chrX-147318813;