rs4128942

chr1-105103104-G-Achr1-105103104-G-Cchr1-105103104-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.598

Alfa AF: 0.634 Hom.: 16362

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

Splicing

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

Publications

LitVar

Other links and lift over

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