rs6990201

Variant names:

• chr8-128592183-C-T
• rs6990201
• ENST00000834545.1:n.403-1971G>A

Variant summary

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

The ENST00000834545.1(ENSG00000308486):​n.403-1971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 151,938 control chromosomes in the GnomAD database, including 4,197 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 0.19 (4197 hom., cov: 32)
• Consequence: ENSG00000308486 ENST00000834545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 1 publications found

Genes affected

ENSG00000308486 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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
ENSG00000308486	ENST00000834545.1	n.403-1971G>A		intron_variant	Intron 1 of 1
ENSG00000308486	ENST00000834546.1	n.396-1971G>A		intron_variant	Intron 2 of 2
ENSG00000308486	ENST00000834547.1	n.375-1971G>A		intron_variant	Intron 2 of 2
ENSG00000308486	ENST00000834548.1	n.233-1946G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29256 AN: 151820 Hom.: 4196 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0799

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0941

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.193 AC: 29279 AN: 151938 Hom.: 4197 Cov.: 32 AF XY: 0.190 AC XY: 14092 AN XY: 74236

African (AFR) AF: 0.404 AC: 16738 AN: 41396

American (AMR) AF: 0.149 AC: 2274 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3468

East Asian (EAS) AF: 0.0798 AC: 412 AN: 5160

South Asian (SAS) AF: 0.108 AC: 520 AN: 4816

European-Finnish (FIN) AF: 0.0941 AC: 994 AN: 10560

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7225 AN: 67968

Other (OTH) AF: 0.184 AC: 389 AN: 2110

Alfa AF: 0.145 Hom.: 5261

Bravo AF: 0.207

Asia WGS AF: 0.102 AC: 355 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.57
DANN	Benign	0.51
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs6990201; hg19: chr8-129604429; COSMIC: COSV67342225;