chr1-145709377-C-T

Variant names:

• chr1-145709377-C-T
• rs12129861

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 0.423 in 152,008 control chromosomes in the GnomAD database, including 13,968 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 0.42 (13968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 61 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 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: 0.423 AC: 64306 AN: 151890 Hom.: 13965 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.423 AC: 64346 AN: 152008 Hom.: 13968 Cov.: 32 AF XY: 0.422 AC XY: 31304 AN XY: 74268

African (AFR) AF: 0.387 AC: 16062 AN: 41468

American (AMR) AF: 0.399 AC: 6089 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3466

East Asian (EAS) AF: 0.184 AC: 951 AN: 5172

South Asian (SAS) AF: 0.301 AC: 1448 AN: 4818

European-Finnish (FIN) AF: 0.485 AC: 5110 AN: 10542

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32082 AN: 67964

Other (OTH) AF: 0.407 AC: 858 AN: 2110

Alfa AF: 0.445 Hom.: 61396

Bravo AF: 0.413

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.46
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs12129861; hg19: chr1-145725689;