rs13106616

Variant names:

• chr4-34041798-G-A
• rs13106616

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 0.192 in 151,950 control chromosomes in the GnomAD database, including 3,889 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 0.19 (3889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 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: 0.192 AC: 29135 AN: 151832 Hom.: 3876 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.192 AC: 29178 AN: 151950 Hom.: 3889 Cov.: 32 AF XY: 0.194 AC XY: 14414 AN XY: 74276

African (AFR) AF: 0.363 AC: 15045 AN: 41422

American (AMR) AF: 0.209 AC: 3192 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1455 AN: 5154

South Asian (SAS) AF: 0.152 AC: 732 AN: 4822

European-Finnish (FIN) AF: 0.111 AC: 1166 AN: 10550

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6663 AN: 67962

Other (OTH) AF: 0.175 AC: 368 AN: 2108

Alfa AF: 0.128 Hom.: 6991

Bravo AF: 0.205

Asia WGS AF: 0.258 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.8
DANN	Benign	0.42
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs13106616; hg19: chr4-34043420;