7-21183171-C-T

Position:

• chr7-21183171-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 0.259 in 151,750 control chromosomes in the GnomAD database, including 5,564 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 0.26 (5564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39214 AN: 151632 Hom.: 5552 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.259 AC: 39264 AN: 151750 Hom.: 5564 Cov.: 32 AF XY: 0.254 AC XY: 18844 AN XY: 74134

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.246

Alfa AF: 0.222 Hom.: 6284

Bravo AF: 0.263

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6971109; hg19: chr7-21222790;