ENST00000440461.3:n.259-576G>A

Variant names:

• chr10-102846879-C-T
• rs7097872
• ENST00000440461.3:n.259-576G>A

Variant summary

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

The ENST00000440461.3(ENSG00000282772):​n.259-576G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,992 control chromosomes in the GnomAD database, including 12,681 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 0.41 (12681 hom., cov: 32)
• Consequence: ENSG00000282772 ENST00000440461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 7 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 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
ENSG00000282772	ENST00000440461.3	n.259-576G>A		intron_variant	Intron 1 of 1	5
ENSG00000282772	ENST00000629474.2	n.382-576G>A		intron_variant	Intron 2 of 2	5
ENSG00000282772	ENST00000631443.1	n.382-938G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61595 AN: 151874 Hom.: 12666 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.406 AC: 61653 AN: 151992 Hom.: 12681 Cov.: 32 AF XY: 0.404 AC XY: 30016 AN XY: 74302

African (AFR) AF: 0.375 AC: 15529 AN: 41440

American (AMR) AF: 0.403 AC: 6159 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3472

East Asian (EAS) AF: 0.563 AC: 2911 AN: 5168

South Asian (SAS) AF: 0.467 AC: 2249 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3784 AN: 10548

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28325 AN: 67964

Other (OTH) AF: 0.411 AC: 866 AN: 2106

Alfa AF: 0.416 Hom.: 1733

Bravo AF: 0.406

Asia WGS AF: 0.468 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.1
DANN	Benign	0.24
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs7097872; hg19: chr10-104606636;