2-47388948-T-C

Variant names:

• chr2-47388948-T-C
• rs6744343

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 0.141 in 152,150 control chromosomes in the GnomAD database, including 1,880 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 0.14 (1880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 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: 0.141 AC: 21470 AN: 152032 Hom.: 1877 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.141 AC: 21501 AN: 152150 Hom.: 1880 Cov.: 31 AF XY: 0.141 AC XY: 10455 AN XY: 74386

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.0880

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.132

Alfa AF: 0.100 Hom.: 885

Bravo AF: 0.144

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6744343; hg19: chr2-47616087;