6-13560602-C-T

Variant names:

• chr6-13560602-C-T
• rs10498683

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 0.158 in 152,218 control chromosomes in the GnomAD database, including 2,130 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 0.16 (2130 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23997 AN: 152100 Hom.: 2125 Cov.: 33

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.158 AC: 24008 AN: 152218 Hom.: 2130 Cov.: 33 AF XY: 0.159 AC XY: 11828 AN XY: 74414

African (AFR) AF: 0.0820 AC: 3407 AN: 41556

American (AMR) AF: 0.144 AC: 2197 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1673 AN: 5180

South Asian (SAS) AF: 0.153 AC: 741 AN: 4828

European-Finnish (FIN) AF: 0.211 AC: 2225 AN: 10568

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12595 AN: 68004

Other (OTH) AF: 0.164 AC: 345 AN: 2108

Alfa AF: 0.170 Hom.: 5473

Bravo AF: 0.152

Asia WGS AF: 0.211 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10498683; hg19: chr6-13560834;