rs6990834

Variant names:

• chr8-114998137-T-C
• rs6990834
• ENST00000791004.1:n.1922T>C

Variant summary

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

The ENST00000791004.1(ENSG00000303006):​n.1922T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,000 control chromosomes in the GnomAD database, including 20,788 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 0.49 (20788 hom., cov: 32)
• Consequence: ENSG00000303006 ENST00000791004.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 1 publications found

Genes affected

ENSG00000303006 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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
ENSG00000303006	ENST00000791004.1	n.1922T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74419 AN: 151882 Hom.: 20792 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.490 AC: 74413 AN: 152000 Hom.: 20788 Cov.: 32 AF XY: 0.484 AC XY: 35989 AN XY: 74298

African (AFR) AF: 0.233 AC: 9661 AN: 41480

American (AMR) AF: 0.458 AC: 6988 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2251 AN: 3468

East Asian (EAS) AF: 0.222 AC: 1150 AN: 5174

South Asian (SAS) AF: 0.536 AC: 2581 AN: 4812

European-Finnish (FIN) AF: 0.595 AC: 6274 AN: 10546

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43598 AN: 67960

Other (OTH) AF: 0.542 AC: 1142 AN: 2106

Alfa AF: 0.545 Hom.: 3189

Bravo AF: 0.469

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.61
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs6990834; hg19: chr8-116010366;