rs12967884

Variant names:

• chr18-78831635-A-G
• rs12967884

Your query was ambiguous. Multiple possible variants found:

• chr18-78831635-A-G
• chr18-78831635-A-T

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 0.161 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.261 AC: 10772 AN: 41344

American (AMR) AF: 0.198 AC: 3020 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3472

East Asian (EAS) AF: 0.177 AC: 915 AN: 5160

South Asian (SAS) AF: 0.119 AC: 572 AN: 4806

European-Finnish (FIN) AF: 0.103 AC: 1087 AN: 10562

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7215 AN: 67926

Other (OTH) AF: 0.154 AC: 325 AN: 2104

Alfa AF: 0.127 Hom.: 4368

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
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs12967884; hg19: chr18-76591635;