1-171289503-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 0.401 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;