rs12605415

Variant names:

• chr18-28301357-G-T
• rs12605415

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 0.339 in 151,826 control chromosomes in the GnomAD database, including 9,414 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 0.34 (9414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.443 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: 0.339 AC: 51500 AN: 151706 Hom.: 9414 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.339 AC: 51507 AN: 151826 Hom.: 9414 Cov.: 32 AF XY: 0.341 AC XY: 25262 AN XY: 74180

African (AFR) AF: 0.193 AC: 7989 AN: 41456

American (AMR) AF: 0.366 AC: 5564 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1493 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5160

South Asian (SAS) AF: 0.459 AC: 2210 AN: 4818

European-Finnish (FIN) AF: 0.337 AC: 3542 AN: 10520

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27090 AN: 67868

Other (OTH) AF: 0.384 AC: 809 AN: 2106

Alfa AF: 0.386 Hom.: 5823

Bravo AF: 0.333

Asia WGS AF: 0.437 AC: 1515 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.24
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs12605415; hg19: chr18-25881321;