6-106336676-T-C

Variant names:

• chr6-106336676-T-C
• rs694433

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 0.324 in 152,006 control chromosomes in the GnomAD database, including 8,664 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 0.32 (8664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49227 AN: 151888 Hom.: 8639 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.324 AC: 49301 AN: 152006 Hom.: 8664 Cov.: 32 AF XY: 0.320 AC XY: 23756 AN XY: 74322

African (AFR) AF: 0.467 AC: 19340 AN: 41430

American (AMR) AF: 0.241 AC: 3678 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1718 AN: 5166

South Asian (SAS) AF: 0.224 AC: 1081 AN: 4820

European-Finnish (FIN) AF: 0.224 AC: 2362 AN: 10566

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18819 AN: 67968

Other (OTH) AF: 0.327 AC: 690 AN: 2112

Alfa AF: 0.294 Hom.: 5615

Bravo AF: 0.332

Asia WGS AF: 0.320 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.8
DANN	Benign	0.38
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs694433; hg19: chr6-106784551; COSMIC: COSV69419355;