chr1-153781249-C-A

Position:

• chr1-153781249-C-A

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 0.342 in 151,974 control chromosomes in the GnomAD database, including 9,268 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 0.34 (9268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 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: 0.342 AC: 51951 AN: 151856 Hom.: 9272 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.342 AC: 51967 AN: 151974 Hom.: 9268 Cov.: 32 AF XY: 0.345 AC XY: 25588 AN XY: 74260

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.368

Alfa AF: 0.373 Hom.: 8730

Bravo AF: 0.345

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.015
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10908474; hg19: chr1-153753725;