2-47388948-T-C

Position:

• chr2-47388948-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;