rs2036138

Variant names:

• chr4-145563710-G-A
• rs2036138

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 0.36 in 152,082 control chromosomes in the GnomAD database, including 11,885 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 0.36 (11885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.361 AC: 54791 AN: 151964 Hom.: 11884 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.360 AC: 54800 AN: 152082 Hom.: 11885 Cov.: 32 AF XY: 0.356 AC XY: 26504 AN XY: 74358

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.352

Alfa AF: 0.402 Hom.: 2257

Bravo AF: 0.334

Asia WGS AF: 0.251 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036138; hg19: chr4-146484862;