7-106178549-C-G

Variant names:

• chr7-106178549-C-G
• rs176574

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 0.335 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.266 AC: 11021 AN: 41470

American (AMR) AF: 0.425 AC: 6490 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1230 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2050 AN: 5144

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4816

European-Finnish (FIN) AF: 0.355 AC: 3748 AN: 10564

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23634 AN: 67970

Other (OTH) AF: 0.361 AC: 764 AN: 2114

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs176574; hg19: chr7-105818995;