rs12606601

Variant names:

• chr18-27707989-G-A
• rs12606601

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 0.0729 in 151,386 control chromosomes in the GnomAD database, including 433 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 0.073 (433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 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: 0.0729 AC: 11026 AN: 151268 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0490

Gnomad SAS AF: 0.0111

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0729 AC: 11038 AN: 151386 Hom.: 433 Cov.: 32 AF XY: 0.0702 AC XY: 5189 AN XY: 73934

African (AFR) AF: 0.104 AC: 4315 AN: 41310

American (AMR) AF: 0.0591 AC: 898 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3466

East Asian (EAS) AF: 0.0487 AC: 248 AN: 5088

South Asian (SAS) AF: 0.0107 AC: 51 AN: 4776

European-Finnish (FIN) AF: 0.0336 AC: 350 AN: 10408

Middle Eastern (MID) AF: 0.0862 AC: 25 AN: 290

European-Non Finnish (NFE) AF: 0.0670 AC: 4542 AN: 67840

Other (OTH) AF: 0.0805 AC: 169 AN: 2100

Alfa AF: 0.0693 Hom.: 859

Bravo AF: 0.0768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.60
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs12606601; hg19: chr18-25287953;