chr1-145711327-T-G

Position:

• chr1-145711327-T-G

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 0.428 in 152,064 control chromosomes in the GnomAD database, including 15,066 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 0.43 (15066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65124 AN: 151946 Hom.: 15065 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.428 AC: 65157 AN: 152064 Hom.: 15066 Cov.: 32 AF XY: 0.427 AC XY: 31745 AN XY: 74310

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.415

Alfa AF: 0.482 Hom.: 4225

Bravo AF: 0.412

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.59
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1471633; hg19: chr1-145723739;