chr20-56248360-G-T

Variant names:

• chr20-56248360-G-T
• rs6127698

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 0.395 in 152,064 control chromosomes in the GnomAD database, including 13,841 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 0.40 (13841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 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: 0.395 AC: 60060 AN: 151946 Hom.: 13834 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.395 AC: 60079 AN: 152064 Hom.: 13841 Cov.: 32 AF XY: 0.396 AC XY: 29439 AN XY: 74330

African (AFR) AF: 0.146 AC: 6076 AN: 41500

American (AMR) AF: 0.519 AC: 7921 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3446 AN: 5164

South Asian (SAS) AF: 0.473 AC: 2272 AN: 4800

European-Finnish (FIN) AF: 0.426 AC: 4508 AN: 10592

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32988 AN: 67950

Other (OTH) AF: 0.444 AC: 937 AN: 2110

Alfa AF: 0.460 Hom.: 12204

Bravo AF: 0.396

Asia WGS AF: 0.526 AC: 1827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.5
DANN	Benign	0.80
PhyloP100		1.2
PromoterAI		-0.00080	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6127698; hg19: chr20-54823416; COSMIC: COSV54763341;