rs2145748

Variant names:

• chr6-44506138-G-A
• rs2145748

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 0.237 in 152,174 control chromosomes in the GnomAD database, including 4,638 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 0.24 (4638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.311 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: 0.237 AC: 35998 AN: 152056 Hom.: 4632 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.237 AC: 36032 AN: 152174 Hom.: 4638 Cov.: 32 AF XY: 0.229 AC XY: 17061 AN XY: 74380

African (AFR) AF: 0.316 AC: 13110 AN: 41506

American (AMR) AF: 0.147 AC: 2254 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3470

East Asian (EAS) AF: 0.0624 AC: 323 AN: 5180

South Asian (SAS) AF: 0.130 AC: 626 AN: 4818

European-Finnish (FIN) AF: 0.202 AC: 2143 AN: 10598

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16466 AN: 67990

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.230 Hom.: 7307

Bravo AF: 0.238

Asia WGS AF: 0.0910 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.69
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs2145748; hg19: chr6-44473875;