rs57024841

Variant names:

• chr9-136968181-G-A
• rs57024841

Your query was ambiguous. Multiple possible variants found:

• chr9-136968181-G-A
• chr9-136968181-G-C

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 0.482 in 152,026 control chromosomes in the GnomAD database, including 19,179 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 0.48 (19179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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: 0.482 AC: 73243 AN: 151914 Hom.: 19185 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.482 AC: 73260 AN: 152026 Hom.: 19179 Cov.: 32 AF XY: 0.484 AC XY: 35980 AN XY: 74330

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.489

Alfa AF: 0.517 Hom.: 2536

Bravo AF: 0.471

Asia WGS AF: 0.317 AC: 1103 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57024841; hg19: chr9-139862633;