rs905238

Variant names:

• chr19-48962127-G-A
• rs905238

Your query was ambiguous. Multiple possible variants found:

• chr19-48962127-G-A
• chr19-48962127-G-T

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 0.563 in 152,034 control chromosomes in the GnomAD database, including 24,247 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 0.56 (24247 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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: 0.563 AC: 85503 AN: 151916 Hom.: 24218 Cov.: 33

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.563 AC: 85583 AN: 152034 Hom.: 24247 Cov.: 33 AF XY: 0.570 AC XY: 42350 AN XY: 74316

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.538

Alfa AF: 0.523 Hom.: 27405

Bravo AF: 0.556

Asia WGS AF: 0.690 AC: 2399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs905238; hg19: chr19-49465384;