8-139167781-G-T

Variant names:

• chr8-139167781-G-T
• rs6997709
• ENST00000797243.1:n.431+1959C>A

Variant summary

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

The ENST00000797243.1(ENSG00000303791):​n.431+1959C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,156 control chromosomes in the GnomAD database, including 4,725 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 (4725 hom., cov: 33)
• Consequence: ENSG00000303791 ENST00000797243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 12 publications found

Genes affected

ENSG00000303791 (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 (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797243.1. 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
	ENSG00000303791	ENST00000797243.1		n.431+1959C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36465 AN: 152038 Hom.: 4724 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.0716

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.240 AC: 36484 AN: 152156 Hom.: 4725 Cov.: 33 AF XY: 0.244 AC XY: 18161 AN XY: 74386

African (AFR) AF: 0.168 AC: 6971 AN: 41508

American (AMR) AF: 0.206 AC: 3146 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3470

East Asian (EAS) AF: 0.0715 AC: 371 AN: 5186

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4820

European-Finnish (FIN) AF: 0.377 AC: 3981 AN: 10556

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19264 AN: 68004

Other (OTH) AF: 0.221 AC: 467 AN: 2114

Alfa AF: 0.257 Hom.: 6546

Bravo AF: 0.219

Asia WGS AF: 0.146 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs6997709; hg19: chr8-140180024;