7-121300382-C-T

Position:

• chr7-121300382-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 0.502 in 152,114 control chromosomes in the GnomAD database, including 22,452 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 0.50 (22452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76270 AN: 151996 Hom.: 22413 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.502 AC: 76363 AN: 152114 Hom.: 22452 Cov.: 32 AF XY: 0.494 AC XY: 36733 AN XY: 74374

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.492

Alfa AF: 0.401 Hom.: 17184

Bravo AF: 0.522

Asia WGS AF: 0.526 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2707521; hg19: chr7-120940436;