rs624097

Variant names:

• chr5-41685242-G-A
• rs624097

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 0.376 in 152,056 control chromosomes in the GnomAD database, including 12,994 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 0.38 (12994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 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: 0.375 AC: 57029 AN: 151938 Hom.: 12958 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0348

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.376 AC: 57121 AN: 152056 Hom.: 12994 Cov.: 32 AF XY: 0.376 AC XY: 27909 AN XY: 74302

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.381

Alfa AF: 0.283 Hom.: 13048

Bravo AF: 0.388

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs624097; hg19: chr5-41685344;