rs10511254

Variant names:

• chr3-106203747-G-A
• rs10511254
• ENST00000667697.1:n.254+1164G>A

Variant summary

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

The ENST00000667697.1(ENSG00000287421):​n.254+1164G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 145,300 control chromosomes in the GnomAD database, including 2,563 homozygotes. 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 0.17 (2563 hom., cov: 29)
• Consequence: ENSG00000287421 ENST00000667697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

ENSG00000287421 (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 (SAS) allele frequency at 95% confidence interval = 0.333 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
ENSG00000287421	ENST00000667697.1	n.254+1164G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 25011 AN: 145168 Hom.: 2560 Cov.: 29

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.172 AC: 25021 AN: 145300 Hom.: 2563 Cov.: 29 AF XY: 0.174 AC XY: 12272 AN XY: 70676

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.174

Alfa AF: 0.189 Hom.: 509

Bravo AF: 0.159

Asia WGS AF: 0.276 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511254; hg19: chr3-105922594;