1-159226975-C-T

Variant names:

• chr1-159226975-C-T
• rs10489849

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 0.302 in 152,088 control chromosomes in the GnomAD database, including 9,208 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 0.30 (9208 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 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: 0.302 AC: 45827 AN: 151970 Hom.: 9201 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.302 AC: 45870 AN: 152088 Hom.: 9208 Cov.: 32 AF XY: 0.299 AC XY: 22245 AN XY: 74346

African (AFR) AF: 0.570 AC: 23655 AN: 41468

American (AMR) AF: 0.251 AC: 3839 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3472

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5184

South Asian (SAS) AF: 0.144 AC: 694 AN: 4830

European-Finnish (FIN) AF: 0.231 AC: 2441 AN: 10572

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

European-Non Finnish (NFE) AF: 0.201 AC: 13691 AN: 67960

Other (OTH) AF: 0.251 AC: 530 AN: 2110

Alfa AF: 0.222 Hom.: 20141

Bravo AF: 0.316

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.54
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10489849; hg19: chr1-159196765;