rs13181236

Variant names:

• chr5-13597977-T-C
• rs13181236

Your query was ambiguous. Multiple possible variants found:

• chr5-13597977-T-C
• chr5-13597977-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 0.573 in 152,018 control chromosomes in the GnomAD database, including 27,087 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 0.57 (27087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 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: 0.574 AC: 87121 AN: 151900 Hom.: 27081 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.573 AC: 87157 AN: 152018 Hom.: 27087 Cov.: 32 AF XY: 0.569 AC XY: 42303 AN XY: 74292

African (AFR) AF: 0.372 AC: 15431 AN: 41436

American (AMR) AF: 0.682 AC: 10408 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2222 AN: 3468

East Asian (EAS) AF: 0.114 AC: 591 AN: 5172

South Asian (SAS) AF: 0.614 AC: 2955 AN: 4816

European-Finnish (FIN) AF: 0.590 AC: 6234 AN: 10560

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47074 AN: 67988

Other (OTH) AF: 0.603 AC: 1274 AN: 2114

Alfa AF: 0.631 Hom.: 5281

Bravo AF: 0.570

Asia WGS AF: 0.411 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.070
DANN	Benign	0.70
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13181236; hg19: chr5-13598086;