1-105103104-G-A

Variant names:

• chr1-105103104-G-A
• rs4128942

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 0.594 in 151,990 control chromosomes in the GnomAD database, including 27,401 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 0.59 (27401 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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: 0.594 AC: 90209 AN: 151870 Hom.: 27393 Cov.: 33

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.594 AC: 90255 AN: 151990 Hom.: 27401 Cov.: 33 AF XY: 0.594 AC XY: 44141 AN XY: 74274

African (AFR) AF: 0.466 AC: 19304 AN: 41464

American (AMR) AF: 0.632 AC: 9644 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2186 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3494 AN: 5150

South Asian (SAS) AF: 0.576 AC: 2778 AN: 4822

European-Finnish (FIN) AF: 0.615 AC: 6488 AN: 10558

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44251 AN: 67952

Other (OTH) AF: 0.598 AC: 1262 AN: 2112

Alfa AF: 0.634 Hom.: 17952

Bravo AF: 0.593

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4128942; hg19: chr1-105645726; COSMIC: COSV59984314;