rs1026942

Positions:

• chr4-27833672-A-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 0.102 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;