rs2442728

Variant names:

• chr6-31351578-G-T
• rs2442728

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 0.371 in 150,192 control chromosomes in the GnomAD database, including 10,658 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 0.37 (10658 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 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: 0.371 AC: 55700 AN: 150074 Hom.: 10648 Cov.: 26

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.371 AC: 55749 AN: 150192 Hom.: 10658 Cov.: 26 AF XY: 0.373 AC XY: 27308 AN XY: 73154

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.373

Alfa AF: 0.389 Hom.: 6735

Bravo AF: 0.373

Asia WGS AF: 0.409 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2442728; hg19: chr6-31319355;