rs6610650

Positions:

• chrX-37777261-G-A

Variant summary

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

The ENST00000465127.1(ENSG00000250349):​c.171+351261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 110,416 control chromosomes in the GnomAD database, including 3,985 homozygotes. There are 8,314 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 0.27 (3985 hom., 8314 hem., cov: 22)
• Consequence: ENSG00000250349 ENST00000465127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200

Genes affected

ENSG00000250349 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37777261G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250349	ENST00000465127.1	c.171+351261G>A		intron_variant		5		ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 29436 AN: 110369 Hom.: 3979 Cov.: 22 AF XY: 0.253 AC XY: 8276 AN XY: 32693

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.267 AC: 29485 AN: 110416 Hom.: 3985 Cov.: 22 AF XY: 0.254 AC XY: 8314 AN XY: 32750

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0693

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.218

Alfa AF: 0.200 Hom.: 5957

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs6610650; hg19: chrX-37636514;