7-106855364-T-C

Variant names:

• chr7-106855364-T-C
• rs17153527

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 0.0959 in 152,214 control chromosomes in the GnomAD database, including 946 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 0.096 (946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14608 AN: 152096 Hom.: 950 Cov.: 32

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0959 AC: 14600 AN: 152214 Hom.: 946 Cov.: 32 AF XY: 0.102 AC XY: 7558 AN XY: 74400

African (AFR) AF: 0.0247 AC: 1028 AN: 41556

American (AMR) AF: 0.0729 AC: 1115 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3470

East Asian (EAS) AF: 0.146 AC: 759 AN: 5182

South Asian (SAS) AF: 0.227 AC: 1097 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2145 AN: 10574

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7562 AN: 68000

Other (OTH) AF: 0.105 AC: 222 AN: 2112

Alfa AF: 0.107 Hom.: 3122

Bravo AF: 0.0813

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.60
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs17153527; hg19: chr7-106495809;