rs1910358

Positions:

• chr5-23907464-C-T

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 0.717 in 151,818 control chromosomes in the GnomAD database, including 39,218 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 0.72 (39218 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 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: 0.717 AC: 108696 AN: 151700 Hom.: 39169 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.717 AC: 108800 AN: 151818 Hom.: 39218 Cov.: 31 AF XY: 0.710 AC XY: 52642 AN XY: 74164

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.717

Alfa AF: 0.733 Hom.: 17944

Bravo AF: 0.714

Asia WGS AF: 0.648 AC: 2232 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.070
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1910358; hg19: chr5-23907573;