chr7-106968592-T-C

Variant names:

• chr7-106968592-T-C
• rs953183

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 0.427 in 152,006 control chromosomes in the GnomAD database, including 14,282 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 0.43 (14282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 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: 0.427 AC: 64848 AN: 151888 Hom.: 14279 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.427 AC: 64869 AN: 152006 Hom.: 14282 Cov.: 32 AF XY: 0.426 AC XY: 31648 AN XY: 74280

African (AFR) AF: 0.342 AC: 14162 AN: 41468

American (AMR) AF: 0.381 AC: 5823 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2322 AN: 5176

South Asian (SAS) AF: 0.427 AC: 2055 AN: 4808

European-Finnish (FIN) AF: 0.496 AC: 5237 AN: 10550

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32406 AN: 67946

Other (OTH) AF: 0.433 AC: 913 AN: 2110

Alfa AF: 0.454 Hom.: 5585

Bravo AF: 0.414

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.70
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs953183; hg19: chr7-106609037;