1-171289503-C-T

Variant names:

• chr1-171289503-C-T
• rs10798304

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 0.401 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.401 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

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.379

Alfa AF: 0.308 Hom.: 7973

Bravo AF: 0.420

Asia WGS AF: 0.332 AC: 1154 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	0.28
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10798304; hg19: chr1-171258642;