1-153780603-T-C

Variant names:

• chr1-153780603-T-C
• rs12030242

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 0.155 in 152,192 control chromosomes in the GnomAD database, including 2,330 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 0.16 (2330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.155 AC: 23602 AN: 152074 Hom.: 2331 Cov.: 32

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.155 AC: 23605 AN: 152192 Hom.: 2330 Cov.: 32 AF XY: 0.159 AC XY: 11821 AN XY: 74420

African (AFR) AF: 0.0752 AC: 3120 AN: 41516

American (AMR) AF: 0.135 AC: 2069 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2518 AN: 5170

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4822

European-Finnish (FIN) AF: 0.208 AC: 2206 AN: 10608

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11576 AN: 67988

Other (OTH) AF: 0.158 AC: 335 AN: 2114

Alfa AF: 0.166 Hom.: 4096

Bravo AF: 0.149

Asia WGS AF: 0.300 AC: 1042 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.54
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12030242; hg19: chr1-153753079;