ENST00000743602.1:n.29+1942C>G

Variant names:

• chr5-111064493-G-C
• rs764916
• ENST00000743602.1:n.29+1942C>G

Variant summary

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

The ENST00000743602.1(ENSG00000296915):​n.29+1942C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,118 control chromosomes in the GnomAD database, including 1,435 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 0.11 (1435 hom., cov: 33)
• Consequence: ENSG00000296915 ENST00000743602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 5 publications found

Genes affected

ENSG00000296915 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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
ENSG00000296915	ENST00000743602.1	n.29+1942C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16814 AN: 152000 Hom.: 1436 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.111 AC: 16821 AN: 152118 Hom.: 1435 Cov.: 33 AF XY: 0.115 AC XY: 8525 AN XY: 74376

African (AFR) AF: 0.194 AC: 8053 AN: 41492

American (AMR) AF: 0.0958 AC: 1464 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1969 AN: 5162

South Asian (SAS) AF: 0.182 AC: 877 AN: 4826

European-Finnish (FIN) AF: 0.0653 AC: 693 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0489 AC: 3321 AN: 67972

Other (OTH) AF: 0.0882 AC: 186 AN: 2108

Alfa AF: 0.0850 Hom.: 119

Bravo AF: 0.116

Asia WGS AF: 0.227 AC: 787 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.36
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs764916; hg19: chr5-110400191;