1-46415681-T-C

Variant names:

• chr1-46415681-T-C
• rs324425

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 0.963 in 152,326 control chromosomes in the GnomAD database, including 70,642 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 0.96 (70642 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.963 AC: 146579 AN: 152208 Hom.: 70604 Cov.: 33

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 0.966

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.963 AC: 146672 AN: 152326 Hom.: 70642 Cov.: 33 AF XY: 0.964 AC XY: 71800 AN XY: 74488

African (AFR) AF: 0.974 AC: 40479 AN: 41556

American (AMR) AF: 0.981 AC: 15014 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.966 AC: 3355 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5159 AN: 5178

South Asian (SAS) AF: 0.952 AC: 4600 AN: 4832

European-Finnish (FIN) AF: 0.979 AC: 10397 AN: 10620

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64467 AN: 68038

Other (OTH) AF: 0.957 AC: 2025 AN: 2116

Alfa AF: 0.953 Hom.: 97910

Bravo AF: 0.964

Asia WGS AF: 0.959 AC: 3335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs324425; hg19: chr1-46881353;