chr1-182052148-C-T

Position:

• chr1-182052148-C-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 0.0848 in 152,172 control chromosomes in the GnomAD database, including 1,183 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 0.085 (1183 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 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: 0.0846 AC: 12869 AN: 152054 Hom.: 1174 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0848 AC: 12904 AN: 152172 Hom.: 1183 Cov.: 32 AF XY: 0.0862 AC XY: 6410 AN XY: 74400

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0562

Gnomad4 ASJ AF: 0.0260

Gnomad4 EAS AF: 0.0571

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0161

Gnomad4 NFE AF: 0.0175

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0358 Hom.: 160

Bravo AF: 0.0905

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	14
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7554182; hg19: chr1-182021283;