rs4149525

Variant names:

• chr4-69860681-T-C
• rs4149525

Your query was ambiguous. Multiple possible variants found:

• chr4-69860681-T-C
• chr4-69860681-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.189 in 152,022 control chromosomes in the GnomAD database, including 2,996 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 (2996 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 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: 0.188 AC: 28622 AN: 151904 Hom.: 2985 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.189 AC: 28672 AN: 152022 Hom.: 2996 Cov.: 31 AF XY: 0.196 AC XY: 14587 AN XY: 74316

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.165

Alfa AF: 0.145 Hom.: 2090

Bravo AF: 0.186

Asia WGS AF: 0.209 AC: 724 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4149525; hg19: chr4-70726399;