ENST00000796877.1:n.163-27156G>A

Variant names:

• chr8-59687722-G-A
• rs6981960
• ENST00000796877.1:n.163-27156G>A

Variant summary

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

The ENST00000796877.1(ENSG00000303742):​n.163-27156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,052 control chromosomes in the GnomAD database, including 11,658 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 0.37 (11658 hom., cov: 32)
• Consequence: ENSG00000303742 ENST00000796877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 3 publications found

Genes affected

ENSG00000303742 (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 = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796877.1. 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
	ENSG00000303742	ENST00000796877.1		n.163-27156G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56873 AN: 151934 Hom.: 11637 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.374 AC: 56943 AN: 152052 Hom.: 11658 Cov.: 32 AF XY: 0.370 AC XY: 27513 AN XY: 74318

African (AFR) AF: 0.562 AC: 23307 AN: 41464

American (AMR) AF: 0.310 AC: 4741 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1489 AN: 5178

South Asian (SAS) AF: 0.308 AC: 1481 AN: 4808

European-Finnish (FIN) AF: 0.263 AC: 2782 AN: 10560

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20736 AN: 67960

Other (OTH) AF: 0.346 AC: 731 AN: 2114

Alfa AF: 0.329 Hom.: 27523

Bravo AF: 0.385

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.68
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6981960; hg19: chr8-60600281;