rs6610650

Variant names:

• chrX-37777261-G-A
• rs6610650
• ENST00000465127.1:c.171+351261G>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250349	ENST00000465127.1	c.171+351261G>A		intron_variant	Intron 3 of 8	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;