6-26556662-G-C

Variant names:

• chr6-26556662-G-C
• rs10484443
• unassigned_transcript_967:c.*44G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000000000(TRK-CTT2-4):​c.*44G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,028 control chromosomes in the GnomAD database, including 408 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 0.056 (408 hom., cov: 32)
• Consequence: TRK-CTT2-4 ENST00000000000 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 4 publications found

Genes affected

TRK-CTT2-4 (HGNC:34671):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.12 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: 0.0564 AC: 8565 AN: 151910 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0208

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0564 AC: 8577 AN: 152028 Hom.: 408 Cov.: 32 AF XY: 0.0577 AC XY: 4291 AN XY: 74338

African (AFR) AF: 0.123 AC: 5088 AN: 41446

American (AMR) AF: 0.0251 AC: 383 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 64 AN: 3472

East Asian (EAS) AF: 0.101 AC: 520 AN: 5164

South Asian (SAS) AF: 0.125 AC: 604 AN: 4814

European-Finnish (FIN) AF: 0.0347 AC: 366 AN: 10560

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0208 AC: 1414 AN: 67972

Other (OTH) AF: 0.0498 AC: 105 AN: 2110

Alfa AF: 0.0122 Hom.: 1

Bravo AF: 0.0565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	0.42
DANN	Benign	0.50
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10484443; hg19: chr6-26556890;