7-83900749-C-T

Variant names:

• chr7-83900749-C-T
• rs701276

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;