7-121300382-C-T

Variant names:

• chr7-121300382-C-T
• rs2707521

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 0.502 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.825 AC: 34236 AN: 41520

American (AMR) AF: 0.395 AC: 6040 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2141 AN: 5176

South Asian (SAS) AF: 0.543 AC: 2619 AN: 4826

European-Finnish (FIN) AF: 0.291 AC: 3072 AN: 10570

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25331 AN: 67952

Other (OTH) AF: 0.492 AC: 1041 AN: 2114

Alfa AF: 0.415 Hom.: 23716

Bravo AF: 0.522

Asia WGS AF: 0.526 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.43
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2707521; hg19: chr7-120940436;