rs12658762

Variant names:

• chr5-18579497-G-T
• rs12658762

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 0.103 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
• Publications: 2 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0348 AC: 1448 AN: 41554

American (AMR) AF: 0.171 AC: 2613 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.113 AC: 582 AN: 5160

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4824

European-Finnish (FIN) AF: 0.0792 AC: 839 AN: 10598

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8383 AN: 68004

Other (OTH) AF: 0.115 AC: 243 AN: 2112

Alfa AF: 0.122 Hom.: 1698

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12658762; hg19: chr5-18579606;