7-21108059-A-C

Position:

• chr7-21108059-A-C

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 0.178 in 152,068 control chromosomes in the GnomAD database, including 2,645 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 (2645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 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: 0.178 AC: 27043 AN: 151950 Hom.: 2642 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.0773

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.178 AC: 27076 AN: 152068 Hom.: 2645 Cov.: 32 AF XY: 0.175 AC XY: 12987 AN XY: 74322

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.0773

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.181

Alfa AF: 0.157 Hom.: 4043

Bravo AF: 0.186

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11974269; hg19: chr7-21147678; COSMIC: COSV57610662;