rs2942337

Variant names:

• chr5-19351242-T-C
• rs2942337

Your query was ambiguous. Multiple possible variants found:

• chr5-19351242-T-C
• chr5-19351242-T-G

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 0.45 in 151,914 control chromosomes in the GnomAD database, including 15,704 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 0.45 (15704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 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: 0.450 AC: 68267 AN: 151796 Hom.: 15697 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.450 AC: 68312 AN: 151914 Hom.: 15704 Cov.: 32 AF XY: 0.451 AC XY: 33466 AN XY: 74240

African (AFR) AF: 0.400 AC: 16606 AN: 41488

American (AMR) AF: 0.523 AC: 7977 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1163 AN: 5170

South Asian (SAS) AF: 0.481 AC: 2321 AN: 4826

European-Finnish (FIN) AF: 0.480 AC: 5058 AN: 10536

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32061 AN: 67868

Other (OTH) AF: 0.441 AC: 931 AN: 2110

Alfa AF: 0.459 Hom.: 2030

Bravo AF: 0.446

Asia WGS AF: 0.394 AC: 1369 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	2.5
DANN	Benign	0.36
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2942337; hg19: chr5-19351351;