3-164184635-C-T

Position:

• chr3-164184635-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 0.221 in 151,984 control chromosomes in the GnomAD database, including 4,033 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 (4033 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

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 (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.164184635C>T		intergenic_region
LOC102724419	XR_001740997.2	n.1103+8873G>A		intron_variant
LOC102724419	XR_007096283.1	n.1103+8873G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33628 AN: 151866 Hom.: 4031 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.221 AC: 33633 AN: 151984 Hom.: 4033 Cov.: 32 AF XY: 0.225 AC XY: 16730 AN XY: 74272

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.221

Alfa AF: 0.225 Hom.: 524

Bravo AF: 0.213

Asia WGS AF: 0.211 AC: 733 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	2.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs710848; hg19: chr3-163902423;