1-67284791-T-C

Variant names:

• chr1-67284791-T-C
• rs7546245

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 0.284 in 151,992 control chromosomes in the GnomAD database, including 7,040 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 0.28 (7040 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.515 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: 0.284 AC: 43103 AN: 151874 Hom.: 7038 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.284 AC: 43134 AN: 151992 Hom.: 7040 Cov.: 31 AF XY: 0.292 AC XY: 21684 AN XY: 74298

African (AFR) AF: 0.148 AC: 6115 AN: 41448

American (AMR) AF: 0.241 AC: 3673 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3468

East Asian (EAS) AF: 0.497 AC: 2569 AN: 5170

South Asian (SAS) AF: 0.532 AC: 2557 AN: 4804

European-Finnish (FIN) AF: 0.424 AC: 4474 AN: 10546

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21654 AN: 67966

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.286 Hom.: 947

Bravo AF: 0.260

Asia WGS AF: 0.468 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.57
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs7546245; hg19: chr1-67750474;