3-95687787-T-C

Position:

• chr3-95687787-T-C

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 0.329 in 152,086 control chromosomes in the GnomAD database, including 8,458 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 0.33 (8458 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95687787T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50065 AN: 151968 Hom.: 8453 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.329 AC: 50092 AN: 152086 Hom.: 8458 Cov.: 32 AF XY: 0.330 AC XY: 24508 AN XY: 74352

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.299

Alfa AF: 0.342 Hom.: 1127

Bravo AF: 0.316

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6806361; hg19: chr3-95406631;