chr1-203188745-C-T

Position:

• chr1-203188745-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 0.477 in 152,054 control chromosomes in the GnomAD database, including 19,959 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 0.48 (19959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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: 0.477 AC: 72525 AN: 151936 Hom.: 19967 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.477 AC: 72514 AN: 152054 Hom.: 19959 Cov.: 32 AF XY: 0.476 AC XY: 35397 AN XY: 74328

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.480

Alfa AF: 0.508 Hom.: 2060

Bravo AF: 0.441

Asia WGS AF: 0.426 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs946261; hg19: chr1-203157873;