1-181855747-T-C

Variant names:

• chr1-181855747-T-C
• rs7533297

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 0.341 in 152,054 control chromosomes in the GnomAD database, including 9,012 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 (9012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.341 AC: 51870 AN: 151936 Hom.: 9001 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.341 AC: 51908 AN: 152054 Hom.: 9012 Cov.: 32 AF XY: 0.341 AC XY: 25375 AN XY: 74314

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.335

Alfa AF: 0.318 Hom.: 10410

Bravo AF: 0.350

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
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: rs7533297; hg19: chr1-181824882;