1-242963050-C-T

Variant names:

• chr1-242963050-C-T
• rs6697552

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.234 AC: 9702 AN: 41490

American (AMR) AF: 0.406 AC: 6194 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 772 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2087 AN: 5156

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4824

European-Finnish (FIN) AF: 0.351 AC: 3714 AN: 10574

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21371 AN: 67932

Other (OTH) AF: 0.321 AC: 677 AN: 2112

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
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs6697552; hg19: chr1-243126352;