7-106178549-C-G

Variant names:

• chr7-106178549-C-G
• rs176574

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 0.335 in 152,038 control chromosomes in the GnomAD database, including 8,954 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 0.34 (8954 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.416 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: 0.335 AC: 50928 AN: 151920 Hom.: 8932 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.335 AC: 51007 AN: 152038 Hom.: 8954 Cov.: 33 AF XY: 0.337 AC XY: 25031 AN XY: 74316

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.361

Alfa AF: 0.139 Hom.: 262

Bravo AF: 0.341

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs176574; hg19: chr7-105818995;