3-182722347-C-T

Position:

• chr3-182722347-C-T

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 0.199 in 152,138 control chromosomes in the GnomAD database, including 3,256 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 0.20 (3256 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.182722347C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30168 AN: 152020 Hom.: 3245 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.199 AC: 30204 AN: 152138 Hom.: 3256 Cov.: 31 AF XY: 0.200 AC XY: 14881 AN XY: 74360

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.204

Alfa AF: 0.177 Hom.: 3218

Bravo AF: 0.207

Asia WGS AF: 0.260 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2700868; hg19: chr3-182440135;