rs13409978

Variant names:

• chr2-42038562-A-C
• rs13409978

Your query was ambiguous. Multiple possible variants found:

• chr2-42038562-A-C
• chr2-42038562-A-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 0.235 in 152,180 control chromosomes in the GnomAD database, including 5,884 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 (5884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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: 0.235 AC: 35687 AN: 152062 Hom.: 5861 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.0760

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.235 AC: 35779 AN: 152180 Hom.: 5884 Cov.: 32 AF XY: 0.234 AC XY: 17441 AN XY: 74422

African (AFR) AF: 0.413 AC: 17137 AN: 41480

American (AMR) AF: 0.373 AC: 5701 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2093 AN: 5172

South Asian (SAS) AF: 0.184 AC: 887 AN: 4830

European-Finnish (FIN) AF: 0.0595 AC: 632 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8507 AN: 68004

Other (OTH) AF: 0.215 AC: 454 AN: 2114

Alfa AF: 0.121 Hom.: 305

Bravo AF: 0.274

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.82
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs13409978; hg19: chr2-42265702;