rs4449553

Variant names:

• chr5-170084454-T-C
• rs4449553

Your query was ambiguous. Multiple possible variants found:

• chr5-170084454-T-C
• chr5-170084454-T-G

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 0.257 in 151,994 control chromosomes in the GnomAD database, including 6,948 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 0.26 (6948 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 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: 0.257 AC: 39012 AN: 151876 Hom.: 6922 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.257 AC: 39088 AN: 151994 Hom.: 6948 Cov.: 31 AF XY: 0.259 AC XY: 19245 AN XY: 74306

African (AFR) AF: 0.491 AC: 20341 AN: 41428

American (AMR) AF: 0.195 AC: 2975 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3468

East Asian (EAS) AF: 0.452 AC: 2319 AN: 5134

South Asian (SAS) AF: 0.245 AC: 1177 AN: 4812

European-Finnish (FIN) AF: 0.190 AC: 2015 AN: 10582

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8904 AN: 67972

Other (OTH) AF: 0.245 AC: 517 AN: 2108

Alfa AF: 0.174 Hom.: 1961

Bravo AF: 0.268

Asia WGS AF: 0.337 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.72
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4449553; hg19: chr5-169511458;