rs176095

chr6-32190542-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.221 in 151,544 control chromosomes in the GnomAD database, including 3,939 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 0.22 (3939 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33540 AN: 151422 Hom.: 3946 Cov.: 30

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.221 AC: 33547 AN: 151544 Hom.: 3939 Cov.: 30 AF XY: 0.214 AC XY: 15804 AN XY: 74018

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.203

Alfa AF: 0.219 Hom.: 5769

Bravo AF: 0.228

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
Cadd	Benign	17
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs176095; hg19: chr6-32158319;