ENST00000738164.1:n.299+3738G>A

Variant names:

• chr10-10094510-G-A
• rs12356435
• ENST00000738164.1:n.299+3738G>A

Variant summary

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

The ENST00000738164.1(ENSG00000296323):​n.299+3738G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,086 control chromosomes in the GnomAD database, including 5,389 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 0.24 (5389 hom., cov: 33)
• Consequence: ENSG00000296323 ENST00000738164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 1 publications found

Genes affected

ENSG00000296323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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
ENSG00000296323	ENST00000738164.1	n.299+3738G>A		intron_variant	Intron 3 of 8
ENSG00000296323	ENST00000738165.1	n.326+3738G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35970 AN: 151968 Hom.: 5387 Cov.: 33

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.237 AC: 35972 AN: 152086 Hom.: 5389 Cov.: 33 AF XY: 0.240 AC XY: 17826 AN XY: 74356

African (AFR) AF: 0.0918 AC: 3809 AN: 41502

American (AMR) AF: 0.209 AC: 3200 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1140 AN: 3472

East Asian (EAS) AF: 0.00752 AC: 39 AN: 5184

South Asian (SAS) AF: 0.257 AC: 1237 AN: 4820

European-Finnish (FIN) AF: 0.416 AC: 4380 AN: 10540

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21279 AN: 67960

Other (OTH) AF: 0.222 AC: 469 AN: 2110

Alfa AF: 0.278 Hom.: 22398

Bravo AF: 0.212

Asia WGS AF: 0.127 AC: 444 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.73
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs12356435; hg19: chr10-10136473;