rs12201676

Variant names:

• chr6-89022382-T-C
• rs12201676

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 0.216 in 152,060 control chromosomes in the GnomAD database, including 3,948 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 0.22 (3948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 17 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 = 0.359 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: 0.216 AC: 32839 AN: 151940 Hom.: 3949 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0671

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.216 AC: 32845 AN: 152060 Hom.: 3948 Cov.: 32 AF XY: 0.216 AC XY: 16039 AN XY: 74308

African (AFR) AF: 0.155 AC: 6412 AN: 41492

American (AMR) AF: 0.174 AC: 2656 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1136 AN: 3462

East Asian (EAS) AF: 0.0669 AC: 346 AN: 5172

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2282 AN: 10566

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17188 AN: 67962

Other (OTH) AF: 0.257 AC: 543 AN: 2112

Alfa AF: 0.240 Hom.: 21675

Bravo AF: 0.206

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.32
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs12201676; hg19: chr6-89732101;