rs12658762

Positions:

• chr5-18579497-G-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 0.103 in 152,208 control chromosomes in the GnomAD database, including 1,039 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 0.10 (1039 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 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: 0.103 AC: 15644 AN: 152090 Hom.: 1034 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.103 AC: 15644 AN: 152208 Hom.: 1039 Cov.: 32 AF XY: 0.105 AC XY: 7789 AN XY: 74404

Gnomad4 AFR AF: 0.0348

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0792

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.115

Alfa AF: 0.125 Hom.: 1376

Bravo AF: 0.103

Asia WGS AF: 0.151 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12658762; hg19: chr5-18579606;