rs1399604

Variant names:

• chr2-136373095-A-C
• rs1399604

Your query was ambiguous. Multiple possible variants found:

• chr2-136373095-A-C
• chr2-136373095-A-T

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 0.323 in 152,020 control chromosomes in the GnomAD database, including 8,198 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 0.32 (8198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49103 AN: 151902 Hom.: 8185 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.323 AC: 49167 AN: 152020 Hom.: 8198 Cov.: 32 AF XY: 0.326 AC XY: 24218 AN XY: 74330

African (AFR) AF: 0.311 AC: 12903 AN: 41444

American (AMR) AF: 0.384 AC: 5870 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3466

East Asian (EAS) AF: 0.523 AC: 2708 AN: 5180

South Asian (SAS) AF: 0.320 AC: 1546 AN: 4824

European-Finnish (FIN) AF: 0.344 AC: 3624 AN: 10548

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20703 AN: 67960

Other (OTH) AF: 0.315 AC: 665 AN: 2110

Alfa AF: 0.316 Hom.: 1593

Bravo AF: 0.327

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1399604; hg19: chr2-137130665;