rs2388436

Variant names:

• chr15-94146424-G-A
• rs2388436

Your query was ambiguous. Multiple possible variants found:

• chr15-94146424-G-A
• chr15-94146424-G-C
• chr15-94146424-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 0.603 in 151,222 control chromosomes in the GnomAD database, including 27,693 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 0.60 (27693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.664 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: 0.603 AC: 91097 AN: 151104 Hom.: 27666 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.603 AC: 91173 AN: 151222 Hom.: 27693 Cov.: 31 AF XY: 0.602 AC XY: 44467 AN XY: 73872

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.651

Alfa AF: 0.541 Hom.: 4668

Bravo AF: 0.609

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388436; hg19: chr15-94689653;