rs13004938

Variant names:

• chr2-5297410-A-G
• rs13004938

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 0.168 in 152,164 control chromosomes in the GnomAD database, including 2,479 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 0.17 (2479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 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: 0.167 AC: 25467 AN: 152046 Hom.: 2470 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.00348

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.168 AC: 25502 AN: 152164 Hom.: 2479 Cov.: 32 AF XY: 0.164 AC XY: 12193 AN XY: 74366

African (AFR) AF: 0.124 AC: 5151 AN: 41544

American (AMR) AF: 0.128 AC: 1962 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3472

East Asian (EAS) AF: 0.00349 AC: 18 AN: 5164

South Asian (SAS) AF: 0.104 AC: 502 AN: 4816

European-Finnish (FIN) AF: 0.182 AC: 1934 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14801 AN: 67970

Other (OTH) AF: 0.164 AC: 346 AN: 2116

Alfa AF: 0.190 Hom.: 4867

Bravo AF: 0.158

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs13004938; hg19: chr2-5437543;