rs4635969

Variant names:

• chr5-1308437-G-A
• rs4635969

Your query was ambiguous. Multiple possible variants found:

• chr5-1308437-G-A
• chr5-1308437-G-C
• chr5-1308437-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 0.217 in 151,916 control chromosomes in the GnomAD database, including 3,930 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 0.22 (3930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

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 (AFR) allele frequency at 95% confidence interval = 0.314 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: 0.217 AC: 32901 AN: 151798 Hom.: 3928 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.217 AC: 32937 AN: 151916 Hom.: 3930 Cov.: 32 AF XY: 0.211 AC XY: 15676 AN XY: 74254

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.200

Alfa AF: 0.195 Hom.: 6411

Bravo AF: 0.224

Asia WGS AF: 0.139 AC: 484 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	2.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4635969; hg19: chr5-1308552;