rs6610650

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250349	ENST00000465127.1	TSL:5	c.171+351261G>A		intron	N/A	ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 29436 AN: 110369 Hom.: 3979 Cov.: 22

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

African (AFR) AF: 0.540 AC: 16305 AN: 30208

American (AMR) AF: 0.216 AC: 2254 AN: 10453

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 535 AN: 2627

East Asian (EAS) AF: 0.0693 AC: 244 AN: 3522

South Asian (SAS) AF: 0.191 AC: 502 AN: 2625

European-Finnish (FIN) AF: 0.123 AC: 716 AN: 5831

Middle Eastern (MID) AF: 0.0948 AC: 20 AN: 211

European-Non Finnish (NFE) AF: 0.161 AC: 8512 AN: 52756

Other (OTH) AF: 0.218 AC: 328 AN: 1502

Alfa AF: 0.223 Hom.: 11637

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.39
PhyloP100		0.20

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: rs6610650; hg19: chrX-37636514;