20-44318326-T-G

Variant names:

• chr20-44318326-T-G
• rs6017317

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 0.301 in 152,014 control chromosomes in the GnomAD database, including 8,420 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 0.30 (8420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 67 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 (AFR) allele frequency at 95% confidence interval = 0.461 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: 0.301 AC: 45706 AN: 151896 Hom.: 8381 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.301 AC: 45809 AN: 152014 Hom.: 8420 Cov.: 32 AF XY: 0.308 AC XY: 22895 AN XY: 74324

African (AFR) AF: 0.466 AC: 19334 AN: 41452

American (AMR) AF: 0.420 AC: 6408 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3464

East Asian (EAS) AF: 0.458 AC: 2370 AN: 5170

South Asian (SAS) AF: 0.416 AC: 2005 AN: 4822

European-Finnish (FIN) AF: 0.228 AC: 2408 AN: 10566

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11537 AN: 67950

Other (OTH) AF: 0.303 AC: 641 AN: 2116

Alfa AF: 0.214 Hom.: 8106

Bravo AF: 0.323

Asia WGS AF: 0.446 AC: 1548 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	0.74
DANN	Benign	0.80
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6017317; hg19: chr20-42946966;