chr4-19052136-G-A

Variant names:

• chr4-19052136-G-A
• rs207338

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 0.51 in 151,914 control chromosomes in the GnomAD database, including 20,106 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 0.51 (20106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.569 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: 0.510 AC: 77394 AN: 151796 Hom.: 20089 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.510 AC: 77456 AN: 151914 Hom.: 20106 Cov.: 32 AF XY: 0.507 AC XY: 37637 AN XY: 74242

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.507

Alfa AF: 0.493 Hom.: 11279

Bravo AF: 0.524

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs207338; hg19: chr4-19053759;