chr2-47388948-T-C

Variant names:

• chr2-47388948-T-C
• rs6744343

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.234 AC: 9700 AN: 41496

American (AMR) AF: 0.0880 AC: 1342 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1211 AN: 5168

South Asian (SAS) AF: 0.134 AC: 648 AN: 4820

European-Finnish (FIN) AF: 0.100 AC: 1062 AN: 10612

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6879 AN: 68010

Other (OTH) AF: 0.132 AC: 278 AN: 2110

Alfa AF: 0.109 Hom.: 1564

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
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs6744343; hg19: chr2-47616087;