20-6418847-T-C

Variant names:

• chr20-6418847-T-C
• rs2876032
• ENST00000831014.1:n.294+1961A>G

Variant summary

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

The ENST00000831014.1(ENSG00000308090):​n.294+1961A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,008 control chromosomes in the GnomAD database, including 41,432 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 0.73 (41432 hom., cov: 32)
• Consequence: ENSG00000308090 ENST00000831014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 10 publications found

Genes affected

ENSG00000308090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831014.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308090	ENST00000831014.1		n.294+1961A>G		intron	N/A
	ENSG00000308090	ENST00000831015.1		n.233-1504A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111593 AN: 151890 Hom.: 41381 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.735 AC: 111704 AN: 152008 Hom.: 41432 Cov.: 32 AF XY: 0.736 AC XY: 54726 AN XY: 74314

African (AFR) AF: 0.814 AC: 33773 AN: 41480

American (AMR) AF: 0.746 AC: 11376 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3470

East Asian (EAS) AF: 0.906 AC: 4691 AN: 5178

South Asian (SAS) AF: 0.703 AC: 3388 AN: 4820

European-Finnish (FIN) AF: 0.722 AC: 7633 AN: 10570

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45977 AN: 67926

Other (OTH) AF: 0.751 AC: 1585 AN: 2110

Alfa AF: 0.693 Hom.: 25644

Bravo AF: 0.745

Asia WGS AF: 0.778 AC: 2705 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.71
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2876032; hg19: chr20-6399494;