rs12198986

Variant names:

• chr6-7719826-G-A
• rs12198986

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 0.376 in 151,948 control chromosomes in the GnomAD database, including 11,678 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 0.38 (11678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 44 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.515 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: 0.376 AC: 57114 AN: 151830 Hom.: 11677 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.376 AC: 57135 AN: 151948 Hom.: 11678 Cov.: 32 AF XY: 0.373 AC XY: 27719 AN XY: 74250

African (AFR) AF: 0.227 AC: 9410 AN: 41426

American (AMR) AF: 0.303 AC: 4633 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1396 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1226 AN: 5172

South Asian (SAS) AF: 0.532 AC: 2565 AN: 4822

European-Finnish (FIN) AF: 0.463 AC: 4877 AN: 10532

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31629 AN: 67938

Other (OTH) AF: 0.355 AC: 750 AN: 2110

Alfa AF: 0.430 Hom.: 64484

Bravo AF: 0.353

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.086
DANN	Benign	0.74
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12198986; hg19: chr6-7720059;