rs1029541

Variant names:

• chr7-84509688-C-T
• rs1029541

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 0.244 in 151,924 control chromosomes in the GnomAD database, including 5,027 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 0.24 (5027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.244 AC: 36980 AN: 151806 Hom.: 5021 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.244 AC: 37021 AN: 151924 Hom.: 5027 Cov.: 32 AF XY: 0.238 AC XY: 17659 AN XY: 74242

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.255

Alfa AF: 0.219 Hom.: 4938

Bravo AF: 0.252

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1029541; hg19: chr7-84139004;