rs12607795

Variant names:

• chr18-60280865-T-C
• rs12607795

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 0.193 in 152,098 control chromosomes in the GnomAD database, including 3,015 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 0.19 (3015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 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: 0.193 AC: 29316 AN: 151980 Hom.: 3013 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.193 AC: 29311 AN: 152098 Hom.: 3015 Cov.: 32 AF XY: 0.191 AC XY: 14192 AN XY: 74356

African (AFR) AF: 0.147 AC: 6089 AN: 41518

American (AMR) AF: 0.178 AC: 2718 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 802 AN: 3462

East Asian (EAS) AF: 0.141 AC: 731 AN: 5188

South Asian (SAS) AF: 0.147 AC: 705 AN: 4780

European-Finnish (FIN) AF: 0.190 AC: 2002 AN: 10548

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15385 AN: 67998

Other (OTH) AF: 0.218 AC: 461 AN: 2112

Alfa AF: 0.218 Hom.: 12636

Bravo AF: 0.190

Asia WGS AF: 0.124 AC: 430 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.77
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs12607795; hg19: chr18-57948098;