1-30555154-A-T

Position:

• chr1-30555154-A-T

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 0.0169 in 152,276 control chromosomes in the GnomAD database, including 146 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 0.017 (146 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

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 (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0169 AC: 2575 AN: 152158 Hom.: 147 Cov.: 33

Gnomad AFR AF: 0.000989

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0109

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00520

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0169 AC: 2570 AN: 152276 Hom.: 146 Cov.: 33 AF XY: 0.0213 AC XY: 1587 AN XY: 74462

Gnomad4 AFR AF: 0.000987

Gnomad4 AMR AF: 0.0108

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.00745

Gnomad4 FIN AF: 0.0984

Gnomad4 NFE AF: 0.00520

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.0110 Hom.: 6

Bravo AF: 0.0119

Asia WGS AF: 0.0650 AC: 226 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	0.22
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924268; hg19: chr1-31028001;