chr6-26556662-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRK-CTT2-4	unassigned_transcript_967	c.*44G>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;