5-41685242-G-A

Variant names:

• chr5-41685242-G-A
• rs624097

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.636 AC: 26381 AN: 41478

American (AMR) AF: 0.348 AC: 5317 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3470

East Asian (EAS) AF: 0.0349 AC: 181 AN: 5184

South Asian (SAS) AF: 0.319 AC: 1537 AN: 4822

European-Finnish (FIN) AF: 0.285 AC: 3000 AN: 10540

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18198 AN: 67972

Other (OTH) AF: 0.381 AC: 803 AN: 2110

Alfa AF: 0.296 Hom.: 31810

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
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs624097; hg19: chr5-41685344;