rs624097

Positions:

• chr5-41685242-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;