6-36690965-T-C

Variant names:

• chr6-36690965-T-C
• rs12191972

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 0.222 in 152,180 control chromosomes in the GnomAD database, including 3,993 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 (3993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 14 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 (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33776 AN: 152062 Hom.: 3979 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.222 AC: 33811 AN: 152180 Hom.: 3993 Cov.: 32 AF XY: 0.218 AC XY: 16239 AN XY: 74414

African (AFR) AF: 0.292 AC: 12111 AN: 41500

American (AMR) AF: 0.180 AC: 2749 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3468

East Asian (EAS) AF: 0.132 AC: 683 AN: 5186

South Asian (SAS) AF: 0.318 AC: 1532 AN: 4822

European-Finnish (FIN) AF: 0.171 AC: 1807 AN: 10598

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13326 AN: 68002

Other (OTH) AF: 0.250 AC: 528 AN: 2108

Alfa AF: 0.208 Hom.: 9749

Bravo AF: 0.221

Asia WGS AF: 0.277 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.6
DANN	Benign	0.52
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12191972; hg19: chr6-36658742;