chr20-44318326-T-G

Variant names:

• chr20-44318326-T-G
• rs6017317

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 0.301 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.303

Alfa AF: 0.216 Hom.: 1240

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6017317; hg19: chr20-42946966;