1-171289503-C-T

Variant names:

• chr1-171289503-C-T
• rs10798304

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 0.401 in 152,168 control chromosomes in the GnomAD database, including 14,984 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 0.40 (14984 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60897 AN: 152052 Hom.: 14934 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.401 AC: 60996 AN: 152168 Hom.: 14984 Cov.: 33 AF XY: 0.397 AC XY: 29578 AN XY: 74414

African (AFR) AF: 0.705 AC: 29259 AN: 41498

American (AMR) AF: 0.361 AC: 5530 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 970 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1198 AN: 5176

South Asian (SAS) AF: 0.338 AC: 1630 AN: 4824

European-Finnish (FIN) AF: 0.261 AC: 2765 AN: 10592

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18629 AN: 67986

Other (OTH) AF: 0.379 AC: 802 AN: 2114

Alfa AF: 0.323 Hom.: 11656

Bravo AF: 0.420

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.38
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10798304; hg19: chr1-171258642;