rs1026942

Variant names:

• chr4-27833672-A-T
• rs1026942

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 0.102 in 152,242 control chromosomes in the GnomAD database, including 896 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 0.10 (896 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 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: 0.102 AC: 15495 AN: 152124 Hom.: 897 Cov.: 31

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0765

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0892

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.102 AC: 15486 AN: 152242 Hom.: 896 Cov.: 31 AF XY: 0.0989 AC XY: 7363 AN XY: 74418

Gnomad4 AFR AF: 0.0470

Gnomad4 AMR AF: 0.0763

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.0894

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.0983

Alfa AF: 0.123 Hom.: 162

Bravo AF: 0.0966

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1026942; hg19: chr4-27835294;