7-21407271-G-T

Variant names:

• chr7-21407271-G-T
• rs12700284

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 0.184 in 151,822 control chromosomes in the GnomAD database, including 2,925 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 0.18 (2925 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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: 0.184 AC: 27972 AN: 151704 Hom.: 2927 Cov.: 29

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.184 AC: 27982 AN: 151822 Hom.: 2925 Cov.: 29 AF XY: 0.183 AC XY: 13599 AN XY: 74180

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.182

Alfa AF: 0.151 Hom.: 1080

Bravo AF: 0.188

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12700284; hg19: chr7-21446889;