1-151982533-C-T

Variant names:

• chr1-151982533-C-T
• rs6678672

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 0.282 in 152,134 control chromosomes in the GnomAD database, including 6,481 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 (6481 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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: 0.282 AC: 42933 AN: 152014 Hom.: 6482 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.282 AC: 42944 AN: 152134 Hom.: 6481 Cov.: 33 AF XY: 0.284 AC XY: 21095 AN XY: 74362

African (AFR) AF: 0.227 AC: 9412 AN: 41506

American (AMR) AF: 0.232 AC: 3550 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1374 AN: 5178

South Asian (SAS) AF: 0.538 AC: 2589 AN: 4814

European-Finnish (FIN) AF: 0.256 AC: 2702 AN: 10554

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20585 AN: 68002

Other (OTH) AF: 0.284 AC: 602 AN: 2116

Alfa AF: 0.276 Hom.: 1337

Bravo AF: 0.273

Asia WGS AF: 0.319 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs6678672; hg19: chr1-151955009;