7-83900749-C-T

Position:

• chr7-83900749-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.292 in 151,886 control chromosomes in the GnomAD database, including 6,715 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 0.29 (6715 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44292 AN: 151770 Hom.: 6698 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.292 AC: 44336 AN: 151886 Hom.: 6715 Cov.: 32 AF XY: 0.288 AC XY: 21402 AN XY: 74232

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.282

Alfa AF: 0.323 Hom.: 16630

Bravo AF: 0.287

Asia WGS AF: 0.348 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs701276; hg19: chr7-83530065;