rs4957048

Variant names:

• chr5-583327-G-A
• rs4957048

Your query was ambiguous. Multiple possible variants found:

• chr5-583327-G-A
• chr5-583327-G-C
• chr5-583327-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 0.156 in 152,244 control chromosomes in the GnomAD database, including 2,203 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 0.16 (2203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734

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 (NFE) allele frequency at 95% confidence interval = 0.205 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: 0.156 AC: 23792 AN: 152126 Hom.: 2197 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.156 AC: 23814 AN: 152244 Hom.: 2203 Cov.: 32 AF XY: 0.156 AC XY: 11594 AN XY: 74426

Gnomad4 AFR AF: 0.0673

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0367

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.139

Alfa AF: 0.190 Hom.: 2306

Bravo AF: 0.154

Asia WGS AF: 0.120 AC: 417 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	1.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4957048; hg19: chr5-583442;