3-160492107-C-T

Variant names:

• chr3-160492107-C-T
• rs2029361

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.148 in 151,952 control chromosomes in the GnomAD database, including 2,143 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 0.15 (2143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22472 AN: 151834 Hom.: 2139 Cov.: 32

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0437

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.148 AC: 22484 AN: 151952 Hom.: 2143 Cov.: 32 AF XY: 0.148 AC XY: 11015 AN XY: 74266

African (AFR) AF: 0.0486 AC: 2012 AN: 41426

American (AMR) AF: 0.0992 AC: 1513 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3464

East Asian (EAS) AF: 0.0438 AC: 227 AN: 5180

South Asian (SAS) AF: 0.119 AC: 575 AN: 4812

European-Finnish (FIN) AF: 0.267 AC: 2812 AN: 10542

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14009 AN: 67964

Other (OTH) AF: 0.147 AC: 309 AN: 2100

Alfa AF: 0.135 Hom.: 400

Bravo AF: 0.130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.54
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2029361; hg19: chr3-160209895;