rs10511254

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000287421 (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 (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
ENSG00000287421	ENST00000837046.1	n.265-1001G>A		intron_variant	Intron 3 of 3
ENSG00000308895	ENST00000837134.1	n.232+5336C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0477 AC: 1859 AN: 38958

American (AMR) AF: 0.184 AC: 2670 AN: 14524

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 660 AN: 3404

East Asian (EAS) AF: 0.206 AC: 944 AN: 4574

South Asian (SAS) AF: 0.347 AC: 1573 AN: 4534

European-Finnish (FIN) AF: 0.146 AC: 1408 AN: 9614

Middle Eastern (MID) AF: 0.239 AC: 65 AN: 272

European-Non Finnish (NFE) AF: 0.230 AC: 15280 AN: 66524

Other (OTH) AF: 0.174 AC: 351 AN: 2012

Alfa AF: 0.185 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
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs10511254; hg19: chr3-105922594;