chr1-242963050-C-T

Position:

• chr1-242963050-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 0.305 in 152,036 control chromosomes in the GnomAD database, including 7,364 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 0.30 (7364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46258 AN: 151918 Hom.: 7356 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.305 AC: 46311 AN: 152036 Hom.: 7364 Cov.: 32 AF XY: 0.308 AC XY: 22918 AN XY: 74300

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.321

Alfa AF: 0.290 Hom.: 1255

Bravo AF: 0.308

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6697552; hg19: chr1-243126352;