rs41502455

Variant names:

• chr5-23572834-T-A
• rs41502455

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 0.165 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.275 AC: 11417 AN: 41504

American (AMR) AF: 0.168 AC: 2572 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3470

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5176

South Asian (SAS) AF: 0.0858 AC: 414 AN: 4826

European-Finnish (FIN) AF: 0.0363 AC: 386 AN: 10624

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8623 AN: 67982

Other (OTH) AF: 0.194 AC: 410 AN: 2110

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
PhyloP100		0.43

Splicing

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

Other links and lift over

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