rs13130787

Variant names:

• chr4-93965880-T-C
• rs13130787

Your query was ambiguous. Multiple possible variants found:

• chr4-93965880-T-C
• chr4-93965880-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 0.35 in 151,826 control chromosomes in the GnomAD database, including 10,222 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 0.35 (10222 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 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: 0.350 AC: 53114 AN: 151708 Hom.: 10224 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.350 AC: 53128 AN: 151826 Hom.: 10222 Cov.: 30 AF XY: 0.343 AC XY: 25447 AN XY: 74190

African (AFR) AF: 0.193 AC: 7992 AN: 41408

American (AMR) AF: 0.317 AC: 4834 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1497 AN: 3464

East Asian (EAS) AF: 0.306 AC: 1575 AN: 5152

South Asian (SAS) AF: 0.276 AC: 1327 AN: 4806

European-Finnish (FIN) AF: 0.400 AC: 4205 AN: 10522

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30324 AN: 67924

Other (OTH) AF: 0.365 AC: 772 AN: 2114

Alfa AF: 0.409 Hom.: 35582

Bravo AF: 0.338

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs13130787; hg19: chr4-94887031;