4-27535029-A-G

Variant names:

• chr4-27535029-A-G
• rs9291501

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 0.195 in 152,040 control chromosomes in the GnomAD database, including 3,562 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 0.19 (3562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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: 0.194 AC: 29539 AN: 151922 Hom.: 3563 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.195 AC: 29579 AN: 152040 Hom.: 3562 Cov.: 32 AF XY: 0.201 AC XY: 14926 AN XY: 74334

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.211

Alfa AF: 0.167 Hom.: 1063

Bravo AF: 0.207

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9291501; hg19: chr4-27536651;