rs1910358

Variant names:

• chr5-23907464-C-T
• rs1910358

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 0.717 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.741 AC: 30694 AN: 41424

American (AMR) AF: 0.624 AC: 9510 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2738 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2852 AN: 5138

South Asian (SAS) AF: 0.689 AC: 3326 AN: 4826

European-Finnish (FIN) AF: 0.680 AC: 7161 AN: 10524

Middle Eastern (MID) AF: 0.738 AC: 214 AN: 290

European-Non Finnish (NFE) AF: 0.738 AC: 50065 AN: 67882

Other (OTH) AF: 0.717 AC: 1508 AN: 2102

Alfa AF: 0.731 Hom.: 73937

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1910358; hg19: chr5-23907573;