rs6981540

Positions:

• chr8-1959689-G-A

Variant summary

Our verdict is Benign. Variant got -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: ENST00000650061.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650061.1	n.1214C>T		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.979

Gnomad4 FIN AF: 0.943

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.888

Alfa AF: 0.899 Hom.: 80858

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6981540; hg19: chr8-1907855;