1-152578849-C-T

Variant names:

• chr1-152578849-C-T
• rs4112787

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 0.664 in 151,528 control chromosomes in the GnomAD database, including 33,627 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 0.66 (33627 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 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: 0.664 AC: 100555 AN: 151412 Hom.: 33589 Cov.: 30

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.664 AC: 100638 AN: 151528 Hom.: 33627 Cov.: 30 AF XY: 0.665 AC XY: 49237 AN XY: 73988

African (AFR) AF: 0.725 AC: 30008 AN: 41368

American (AMR) AF: 0.636 AC: 9528 AN: 14990

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2161 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3082 AN: 5136

South Asian (SAS) AF: 0.632 AC: 3043 AN: 4816

European-Finnish (FIN) AF: 0.662 AC: 6956 AN: 10512

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43826 AN: 67924

Other (OTH) AF: 0.630 AC: 1327 AN: 2108

Alfa AF: 0.651 Hom.: 7702

Bravo AF: 0.661

Asia WGS AF: 0.598 AC: 2081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.18
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs4112787; hg19: chr1-152551325;