rs1484170

Variant names:

• chr10-80939735-T-C
• rs1484170

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 0.171 in 151,920 control chromosomes in the GnomAD database, including 2,380 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 0.17 (2380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 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: 0.171 AC: 26020 AN: 151802 Hom.: 2376 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.171 AC: 26039 AN: 151920 Hom.: 2380 Cov.: 32 AF XY: 0.169 AC XY: 12522 AN XY: 74238

African (AFR) AF: 0.178 AC: 7370 AN: 41432

American (AMR) AF: 0.146 AC: 2223 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3472

East Asian (EAS) AF: 0.0196 AC: 101 AN: 5154

South Asian (SAS) AF: 0.161 AC: 772 AN: 4808

European-Finnish (FIN) AF: 0.156 AC: 1638 AN: 10530

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12709 AN: 67952

Other (OTH) AF: 0.173 AC: 365 AN: 2106

Alfa AF: 0.178 Hom.: 8735

Bravo AF: 0.168

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.5
DANN	Benign	0.77
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1484170; hg19: chr10-82699491;