rs2244020

Variant names:

• chr6-31379674-A-G
• rs2244020

Variant summary

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

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 0.54 (17829 hom., cov: 18)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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: 0.543 AC: 64976 AN: 119748 Hom.: 17835 Cov.: 18

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.681

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.542 AC: 64965 AN: 119754 Hom.: 17829 Cov.: 18 AF XY: 0.546 AC XY: 31223 AN XY: 57180

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.598

Alfa AF: 0.415 Hom.: 7068

Asia WGS AF: 0.386 AC: 1130 AN: 2932

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244020; hg19: chr6-31347451;