7-8959451-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 0.209 in 152,018 control chromosomes in the GnomAD database, including 3,798 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 0.21 (3798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31699 AN: 151900 Hom.: 3792 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.209 AC: 31713 AN: 152018 Hom.: 3798 Cov.: 32 AF XY: 0.212 AC XY: 15760 AN XY: 74296

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.213

Alfa AF: 0.218 Hom.: 2299

Bravo AF: 0.208

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.6
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16874905; hg19: chr7-8999081;