chr8-1959689-G-A

Variant names:

• chr8-1959689-G-A
• rs6981540
• ENST00000650061.1:n.1214C>T

Variant summary

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

The ENST00000650061.1(ENSG00000285957):​n.1214C>T 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 0.896 in 152,268 control chromosomes in the GnomAD database, including 61,324 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 0.90 (61324 hom., cov: 32)
• Consequence: ENSG00000285957 ENST00000650061.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 6 publications found

Genes affected

ENSG00000285957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000285957	ENST00000650061.1	n.1214C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136403 AN: 152150 Hom.: 61284 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.896 AC: 136500 AN: 152268 Hom.: 61324 Cov.: 32 AF XY: 0.903 AC XY: 67190 AN XY: 74444

African (AFR) AF: 0.852 AC: 35404 AN: 41536

American (AMR) AF: 0.911 AC: 13940 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3167 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5160 AN: 5170

South Asian (SAS) AF: 0.979 AC: 4727 AN: 4826

European-Finnish (FIN) AF: 0.943 AC: 10008 AN: 10618

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61060 AN: 68026

Other (OTH) AF: 0.888 AC: 1877 AN: 2114

Alfa AF: 0.898 Hom.: 96740

Bravo AF: 0.892

Asia WGS AF: 0.975 AC: 3391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6981540; hg19: chr8-1907855;