8-2202177-C-G

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 0.105 in 152,138 control chromosomes in the GnomAD database, including 1,407 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 0.10 (1407 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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: 0.105 AC: 15927 AN: 152020 Hom.: 1403 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0437

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0958

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.105 AC: 15944 AN: 152138 Hom.: 1407 Cov.: 33 AF XY: 0.105 AC XY: 7836 AN XY: 74370

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0437

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0497

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0812 Hom.: 105

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478960; hg19: chr8-2149816;