1-104004198-C-T

Variant names:

• chr1-104004198-C-T
• rs1330408

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 0.45 in 151,732 control chromosomes in the GnomAD database, including 16,114 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 0.45 (16114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 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: 0.450 AC: 68280 AN: 151614 Hom.: 16097 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.450 AC: 68339 AN: 151732 Hom.: 16114 Cov.: 32 AF XY: 0.453 AC XY: 33613 AN XY: 74146

African (AFR) AF: 0.350 AC: 14483 AN: 41430

American (AMR) AF: 0.593 AC: 9020 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3464

East Asian (EAS) AF: 0.710 AC: 3642 AN: 5130

South Asian (SAS) AF: 0.393 AC: 1896 AN: 4820

European-Finnish (FIN) AF: 0.452 AC: 4758 AN: 10520

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31792 AN: 67860

Other (OTH) AF: 0.456 AC: 961 AN: 2108

Alfa AF: 0.420 Hom.: 4206

Bravo AF: 0.461

Asia WGS AF: 0.510 AC: 1768 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.65
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1330408; hg19: chr1-104546820;