ENST00000741195.1:n.65+28651A>C

Variant names:

• chr8-31467803-A-C
• rs1369887
• ENST00000741195.1:n.65+28651A>C

Variant summary

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

The ENST00000741195.1(ENSG00000296688):​n.65+28651A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,056 control chromosomes in the GnomAD database, including 39,690 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 0.72 (39690 hom., cov: 32)
• Consequence: ENSG00000296688 ENST00000741195.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 1 publications found

Genes affected

ENSG00000296688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741195.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296688	ENST00000741195.1		n.65+28651A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109526 AN: 151938 Hom.: 39653 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.721 AC: 109622 AN: 152056 Hom.: 39690 Cov.: 32 AF XY: 0.721 AC XY: 53594 AN XY: 74322

African (AFR) AF: 0.769 AC: 31924 AN: 41494

American (AMR) AF: 0.702 AC: 10724 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3470

East Asian (EAS) AF: 0.607 AC: 3128 AN: 5156

South Asian (SAS) AF: 0.649 AC: 3129 AN: 4822

European-Finnish (FIN) AF: 0.754 AC: 7969 AN: 10566

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47744 AN: 67950

Other (OTH) AF: 0.694 AC: 1464 AN: 2110

Alfa AF: 0.695 Hom.: 19216

Bravo AF: 0.723

Asia WGS AF: 0.602 AC: 2096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.46
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1369887; hg19: chr8-31325319;