chr20-7674331-T-C

Variant names:

• chr20-7674331-T-C
• rs2064267
• ENST00000839999.1:n.397-5332A>G

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.397-5332A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,200 control chromosomes in the GnomAD database, including 54,001 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 0.84 (54001 hom., cov: 32)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975
• Publications: 2 publications found

Genes affected

ENSG00000309276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000309276	ENST00000839999.1	n.397-5332A>G		intron_variant	Intron 3 of 4
ENSG00000309276	ENST00000840000.1	n.76-5332A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127724 AN: 152082 Hom.: 53964 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.840 AC: 127815 AN: 152200 Hom.: 54001 Cov.: 32 AF XY: 0.843 AC XY: 62734 AN XY: 74418

African (AFR) AF: 0.760 AC: 31546 AN: 41506

American (AMR) AF: 0.892 AC: 13646 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2849 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5177 AN: 5182

South Asian (SAS) AF: 0.947 AC: 4571 AN: 4826

European-Finnish (FIN) AF: 0.839 AC: 8884 AN: 10590

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58331 AN: 68018

Other (OTH) AF: 0.842 AC: 1779 AN: 2114

Alfa AF: 0.825 Hom.: 7230

Bravo AF: 0.840

Asia WGS AF: 0.962 AC: 3341 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.72
DANN	Benign	0.80
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs2064267; hg19: chr20-7654978;