6-36651044-C-T

Variant names:

• chr6-36651044-C-T
• rs1321313

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 0.225 in 152,090 control chromosomes in the GnomAD database, including 3,858 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 (3858 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -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 = 0.301 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: 0.225 AC: 34199 AN: 151972 Hom.: 3851 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.225 AC: 34211 AN: 152090 Hom.: 3858 Cov.: 32 AF XY: 0.221 AC XY: 16466 AN XY: 74352

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.264

Alfa AF: 0.241 Hom.: 6191

Bravo AF: 0.220

Asia WGS AF: 0.267 AC: 930 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	0.61
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321313; hg19: chr6-36618821;