3-163978652-C-G

Position:

• chr3-163978652-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 0.296 in 151,918 control chromosomes in the GnomAD database, including 7,384 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 0.30 (7384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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 (EAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44930 AN: 151800 Hom.: 7373 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.296 AC: 44960 AN: 151918 Hom.: 7384 Cov.: 32 AF XY: 0.299 AC XY: 22231 AN XY: 74236

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.346

Alfa AF: 0.297 Hom.: 849

Bravo AF: 0.299

Asia WGS AF: 0.477 AC: 1658 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4352381; hg19: chr3-163696440;