rs41502455

chr5-23572834-T-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 0.165 in 152,174 control chromosomes in the GnomAD database, including 2,577 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 0.16 (2577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24993 AN: 152056 Hom.: 2559 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.0849

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.165 AC: 25066 AN: 152174 Hom.: 2577 Cov.: 32 AF XY: 0.159 AC XY: 11838 AN XY: 74414

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.0858

Gnomad4 FIN AF: 0.0363

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.194

Alfa AF: 0.144 Hom.: 224

Bravo AF: 0.179

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.98
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41502455; hg19: chr5-23572943; COSMIC: COSV67681125;