chrX-37753178-C-T

Variant names:

• chrX-37753178-C-T
• rs72619425
• ENST00000465127.1:c.171+327178C>T

Variant summary

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

The ENST00000465127.1(ENSG00000250349):​c.171+327178C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 110,348 control chromosomes in the GnomAD database, including 1,972 homozygotes. There are 6,420 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 0.21 (1972 hom., 6420 hem., cov: 22)
• Consequence: ENSG00000250349 ENST00000465127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 1 publications found

Genes affected

ENSG00000250349 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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
ENSG00000250349	ENST00000465127.1	c.171+327178C>T		intron_variant	Intron 3 of 8	5		ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 22795 AN: 110294 Hom.: 1969 Cov.: 22

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0698

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.207 AC: 22817 AN: 110348 Hom.: 1972 Cov.: 22 AF XY: 0.197 AC XY: 6420 AN XY: 32652

African (AFR) AF: 0.328 AC: 9915 AN: 30187

American (AMR) AF: 0.194 AC: 2027 AN: 10429

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 527 AN: 2626

East Asian (EAS) AF: 0.0691 AC: 243 AN: 3516

South Asian (SAS) AF: 0.193 AC: 505 AN: 2622

European-Finnish (FIN) AF: 0.132 AC: 766 AN: 5803

Middle Eastern (MID) AF: 0.103 AC: 22 AN: 214

European-Non Finnish (NFE) AF: 0.160 AC: 8465 AN: 52766

Other (OTH) AF: 0.183 AC: 276 AN: 1505

Alfa AF: 0.213 Hom.: 1295

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.47
PhyloP100		-2.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs72619425; hg19: chrX-37612431;