rs12967884

Positions:

• chr18-78831635-A-G
• chr18-78831635-A-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 0.161 in 151,840 control chromosomes in the GnomAD database, including 2,358 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 0.16 (2358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 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: 0.161 AC: 24401 AN: 151720 Hom.: 2357 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.161 AC: 24430 AN: 151840 Hom.: 2358 Cov.: 32 AF XY: 0.160 AC XY: 11884 AN XY: 74208

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.154

Alfa AF: 0.118 Hom.: 1441

Bravo AF: 0.176

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12967884; hg19: chr18-76591635;