20-6642727-T-C

Variant names:

• chr20-6642727-T-C
• rs979012

Variant summary

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

The variant allele was found at a frequency of 0.674 in 152,022 control chromosomes in the GnomAD database, including 34,772 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 0.67 (34772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 44 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 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: 0.674 AC: 102322 AN: 151904 Hom.: 34722 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.674 AC: 102428 AN: 152022 Hom.: 34772 Cov.: 32 AF XY: 0.676 AC XY: 50207 AN XY: 74318

African (AFR) AF: 0.681 AC: 28225 AN: 41466

American (AMR) AF: 0.752 AC: 11478 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1937 AN: 3470

East Asian (EAS) AF: 0.896 AC: 4625 AN: 5164

South Asian (SAS) AF: 0.550 AC: 2650 AN: 4816

European-Finnish (FIN) AF: 0.709 AC: 7503 AN: 10578

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43805 AN: 67954

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

Alfa AF: 0.655 Hom.: 103640

Bravo AF: 0.680

Asia WGS AF: 0.701 AC: 2439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.7
DANN	Benign	0.64
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs979012; hg19: chr20-6623374;