rs4413548

Variant names:

• chr5-177986658-C-T
• rs4413548

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.605 in 151,894 control chromosomes in the GnomAD database, including 28,259 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 0.61 (28259 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.657 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: 0.605 AC: 91865 AN: 151776 Hom.: 28255 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.605 AC: 91910 AN: 151894 Hom.: 28259 Cov.: 31 AF XY: 0.605 AC XY: 44855 AN XY: 74194

African (AFR) AF: 0.539 AC: 22304 AN: 41396

American (AMR) AF: 0.564 AC: 8606 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2024 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2233 AN: 5154

South Asian (SAS) AF: 0.497 AC: 2389 AN: 4806

European-Finnish (FIN) AF: 0.693 AC: 7308 AN: 10542

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45010 AN: 67958

Other (OTH) AF: 0.580 AC: 1227 AN: 2114

Alfa AF: 0.630 Hom.: 102951

Bravo AF: 0.589

Asia WGS AF: 0.474 AC: 1652 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	2.3
DANN	Benign	0.68
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs4413548; hg19: chr5-177413659;