ENST00000779031.1:n.496-2241G>A

Variant names:

• chr10-32146925-G-A
• rs9299674
• ENST00000779031.1:n.496-2241G>A

Variant summary

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

The ENST00000779031.1(ENSG00000301470):​n.496-2241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,220 control chromosomes in the GnomAD database, including 8,927 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 0.34 (8927 hom., cov: 30)
• Consequence: ENSG00000301470 ENST00000779031.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 4 publications found

Genes affected

ENSG00000301470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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
ENSG00000301470	ENST00000779031.1	n.496-2241G>A		intron_variant	Intron 2 of 2
ENSG00000301470	ENST00000779032.1	n.320-2241G>A		intron_variant	Intron 1 of 1
ENSG00000301470	ENST00000779033.1	n.189-2241G>A		intron_variant	Intron 1 of 1
ENSG00000301489	ENST00000779267.1	n.282+46C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51435 AN: 151102 Hom.: 8909 Cov.: 30

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.341 AC: 51509 AN: 151220 Hom.: 8927 Cov.: 30 AF XY: 0.339 AC XY: 25012 AN XY: 73890

African (AFR) AF: 0.407 AC: 16720 AN: 41108

American (AMR) AF: 0.255 AC: 3872 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2052 AN: 5124

South Asian (SAS) AF: 0.308 AC: 1479 AN: 4796

European-Finnish (FIN) AF: 0.284 AC: 2968 AN: 10440

Middle Eastern (MID) AF: 0.307 AC: 89 AN: 290

European-Non Finnish (NFE) AF: 0.327 AC: 22190 AN: 67808

Other (OTH) AF: 0.327 AC: 688 AN: 2102

Alfa AF: 0.329 Hom.: 36017

Bravo AF: 0.343

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.42
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs9299674; hg19: chr10-32435853;