rs1336938

Variant names:

• chr13-88918751-C-A
• rs1336938

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 0.145 in 151,588 control chromosomes in the GnomAD database, including 2,047 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 0.14 (2047 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.145 AC: 21952 AN: 151470 Hom.: 2046 Cov.: 31

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.00310

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.145 AC: 21961 AN: 151588 Hom.: 2047 Cov.: 31 AF XY: 0.145 AC XY: 10762 AN XY: 74100

African (AFR) AF: 0.0522 AC: 2159 AN: 41340

American (AMR) AF: 0.102 AC: 1541 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3458

East Asian (EAS) AF: 0.00311 AC: 16 AN: 5152

South Asian (SAS) AF: 0.103 AC: 494 AN: 4816

European-Finnish (FIN) AF: 0.290 AC: 3040 AN: 10492

Middle Eastern (MID) AF: 0.128 AC: 37 AN: 290

European-Non Finnish (NFE) AF: 0.204 AC: 13818 AN: 67856

Other (OTH) AF: 0.125 AC: 263 AN: 2102

Alfa AF: 0.165 Hom.: 414

Bravo AF: 0.128

Asia WGS AF: 0.0470 AC: 164 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.51
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1336938; hg19: chr13-89571005;