rs10487741

Variant names:

• chr7-38292693-C-T
• rs10487741

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 0.0448 in 151,096 control chromosomes in the GnomAD database, including 427 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 0.045 (427 hom., cov: 27)
• Consequence: TRG intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 3 publications found

Genes affected

TRG (HGNC:12271):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRG		n.38292693C>T		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6759 AN: 150978 Hom.: 429 Cov.: 27

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.0292

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00334

Gnomad FIN AF: 0.000191

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.00496

Gnomad OTH AF: 0.0443

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

GnomAD4 genome AF: 0.0448 AC: 6770 AN: 151096 Hom.: 427 Cov.: 27 AF XY: 0.0432 AC XY: 3187 AN XY: 73818

African (AFR) AF: 0.143 AC: 5857 AN: 40946

American (AMR) AF: 0.0219 AC: 330 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.0292 AC: 101 AN: 3458

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00355 AC: 17 AN: 4784

European-Finnish (FIN) AF: 0.000191 AC: 2 AN: 10458

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.00496 AC: 337 AN: 67890

Other (OTH) AF: 0.0439 AC: 92 AN: 2098

Alfa AF: 0.0255 Hom.: 79

Bravo AF: 0.0520

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		-0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10487741; hg19: chr7-38332294;