20-7674331-T-C

Variant names:

• chr20-7674331-T-C
• rs2064267

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.842

Alfa AF: 0.827 Hom.: 6997

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2064267; hg19: chr20-7654978;