chr1-46392904-T-C

Variant names:

• chr1-46392904-T-C
• rs913168

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 0.414 in 151,728 control chromosomes in the GnomAD database, including 13,244 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 0.41 (13244 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 8 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 = 0.487 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: 0.414 AC: 62793 AN: 151610 Hom.: 13209 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.414 AC: 62864 AN: 151728 Hom.: 13244 Cov.: 31 AF XY: 0.413 AC XY: 30602 AN XY: 74148

African (AFR) AF: 0.470 AC: 19451 AN: 41350

American (AMR) AF: 0.321 AC: 4895 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1171 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1694 AN: 5142

South Asian (SAS) AF: 0.504 AC: 2418 AN: 4798

European-Finnish (FIN) AF: 0.383 AC: 4038 AN: 10542

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27880 AN: 67874

Other (OTH) AF: 0.415 AC: 874 AN: 2106

Alfa AF: 0.397 Hom.: 1540

Bravo AF: 0.409

Asia WGS AF: 0.397 AC: 1382 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	2.7
DANN	Benign	0.36
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs913168; hg19: chr1-46858576;