chr6-36690965-T-C

Position:

• chr6-36690965-T-C

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 0.222 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

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 (SAS) allele frequency at 95% confidence interval = 0.304 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: 0.222 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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.250

Alfa AF: 0.207 Hom.: 3574

Bravo AF: 0.221

Asia WGS AF: 0.277 AC: 962 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	6.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12191972; hg19: chr6-36658742;