7-106771412-T-C

Variant names:

• chr7-106771412-T-C
• rs17477177

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 0.174 in 151,748 control chromosomes in the GnomAD database, including 2,722 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 0.17 (2722 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

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 (SAS) allele frequency at 95% confidence interval = 0.286 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: 0.174 AC: 26330 AN: 151632 Hom.: 2723 Cov.: 30

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.174 AC: 26335 AN: 151748 Hom.: 2722 Cov.: 30 AF XY: 0.180 AC XY: 13339 AN XY: 74120

Gnomad4 AFR AF: 0.0733

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.189

Alfa AF: 0.197 Hom.: 5414

Bravo AF: 0.153

Asia WGS AF: 0.221 AC: 768 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	3.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17477177; hg19: chr7-106411858;