rs2741690

Variant names:

• chr8-6926695-C-G
• rs2741690
• ENST00000734108.1:n.367-101C>G

Variant summary

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

The ENST00000734108.1(ENSG00000295932):​n.367-101C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,278 control chromosomes in the GnomAD database, including 54,984 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 0.85 (54984 hom., cov: 34)
• Consequence: ENSG00000295932 ENST00000734108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 1 publications found

Genes affected

ENSG00000295932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 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
ENSG00000295932	ENST00000734108.1	n.367-101C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128876 AN: 152162 Hom.: 54941 Cov.: 34

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.847 AC: 128977 AN: 152278 Hom.: 54984 Cov.: 34 AF XY: 0.843 AC XY: 62786 AN XY: 74448

African (AFR) AF: 0.941 AC: 39131 AN: 41568

American (AMR) AF: 0.812 AC: 12427 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3057 AN: 3468

East Asian (EAS) AF: 0.844 AC: 4376 AN: 5182

South Asian (SAS) AF: 0.786 AC: 3789 AN: 4822

European-Finnish (FIN) AF: 0.749 AC: 7931 AN: 10582

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55451 AN: 68024

Other (OTH) AF: 0.846 AC: 1790 AN: 2116

Alfa AF: 0.830 Hom.: 6535

Bravo AF: 0.855

Asia WGS AF: 0.845 AC: 2939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.45
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2741690; hg19: chr8-6784217;