10-102851169-G-T

Variant names:

• chr10-102851169-G-T
• rs4290163
• ENST00000440461.3:n.258+3086C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000631443.1(ENSG00000282772):​n.381+339C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,730 control chromosomes in the GnomAD database, including 11,948 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 0.39 (11948 hom., cov: 31)
• Consequence: ENSG00000282772 ENST00000631443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 25 publications found

Genes affected

ENSG00000282772 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631443.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282772	ENST00000440461.3	TSL:5	n.258+3086C>A		intron	N/A
	ENSG00000282772	ENST00000629474.2	TSL:5	n.381+339C>A		intron	N/A
	ENSG00000282772	ENST00000631443.1	TSL:4	n.381+339C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59622 AN: 151612 Hom.: 11937 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.393 AC: 59675 AN: 151730 Hom.: 11948 Cov.: 31 AF XY: 0.391 AC XY: 29010 AN XY: 74128

African (AFR) AF: 0.339 AC: 14036 AN: 41352

American (AMR) AF: 0.394 AC: 6010 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3468

East Asian (EAS) AF: 0.560 AC: 2894 AN: 5164

South Asian (SAS) AF: 0.438 AC: 2102 AN: 4802

European-Finnish (FIN) AF: 0.359 AC: 3760 AN: 10480

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28221 AN: 67920

Other (OTH) AF: 0.401 AC: 842 AN: 2098

Alfa AF: 0.397 Hom.: 13783

Bravo AF: 0.393

Asia WGS AF: 0.454 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.59
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs4290163; hg19: chr10-104610926;