rs13120244

Variant names:

• chr4-110683188-G-A
• rs13120244

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0743 in 152,188 control chromosomes in the GnomAD database, including 598 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 0.074 (598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 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: 0.0744 AC: 11312 AN: 152070 Hom.: 596 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0743 AC: 11308 AN: 152188 Hom.: 598 Cov.: 32 AF XY: 0.0728 AC XY: 5414 AN XY: 74416

African (AFR) AF: 0.0185 AC: 768 AN: 41556

American (AMR) AF: 0.0718 AC: 1097 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.132 AC: 637 AN: 4820

European-Finnish (FIN) AF: 0.0814 AC: 863 AN: 10606

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7194 AN: 67972

Other (OTH) AF: 0.0884 AC: 186 AN: 2104

Alfa AF: 0.0938 Hom.: 571

Bravo AF: 0.0715

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	21
DANN	Benign	0.68
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs13120244; hg19: chr4-111604344;