chr3-101901838-A-G

Variant names:

• chr3-101901838-A-G
• rs771574
• ENST00000657494.1:n.226+15006A>G

Variant summary

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

The ENST00000657494.1(ENSG00000287682):​n.226+15006A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,982 control chromosomes in the GnomAD database, including 6,282 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 0.28 (6282 hom., cov: 32)
• Consequence: ENSG00000287682 ENST00000657494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

Genes affected

ENSG00000287682 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 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
ENSG00000287682	ENST00000657494.1	n.226+15006A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42347 AN: 151864 Hom.: 6284 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.279 AC: 42368 AN: 151982 Hom.: 6282 Cov.: 32 AF XY: 0.275 AC XY: 20407 AN XY: 74290

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.269

Alfa AF: 0.317 Hom.: 13055

Bravo AF: 0.278

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs771574; hg19: chr3-101620682;