rs1605141

chr5-91624144-G-Achr5-91624144-G-C

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 0.424 in 151,228 control chromosomes in the GnomAD database, including 14,512 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 0.42 (14512 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

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 (EAS) allele frequency at 95% confidence interval = 0.529 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: 0.424 AC: 64074 AN: 151112 Hom.: 14514 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.424 AC: 64083 AN: 151228 Hom.: 14512 Cov.: 31 AF XY: 0.427 AC XY: 31539 AN XY: 73868

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.443

Alfa AF: 0.454 Hom.: 2021

Bravo AF: 0.418

Asia WGS AF: 0.416 AC: 1444 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.094
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1605141; hg19: chr5-90919961;