rs13007964

Variant names:

• chr2-238206001-C-T
• rs13007964

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 0.276 in 152,058 control chromosomes in the GnomAD database, including 6,199 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 0.28 (6199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41972 AN: 151940 Hom.: 6194 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.276 AC: 41987 AN: 152058 Hom.: 6199 Cov.: 32 AF XY: 0.276 AC XY: 20534 AN XY: 74298

African (AFR) AF: 0.177 AC: 7350 AN: 41496

American (AMR) AF: 0.253 AC: 3869 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1088 AN: 5170

South Asian (SAS) AF: 0.367 AC: 1771 AN: 4822

European-Finnish (FIN) AF: 0.335 AC: 3529 AN: 10532

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22629 AN: 67970

Other (OTH) AF: 0.270 AC: 570 AN: 2112

Alfa AF: 0.309 Hom.: 954

Bravo AF: 0.266

Asia WGS AF: 0.275 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.43
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs13007964; hg19: chr2-239114642;