chr7-121300382-C-T

Variant names:

• chr7-121300382-C-T
• rs2707521

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;