5-63300149-T-G

Variant names:

• chr5-63300149-T-G
• rs4700575

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 0.245 in 151,834 control chromosomes in the GnomAD database, including 5,253 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 0.24 (5253 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.383 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37105 AN: 151718 Hom.: 5244 Cov.: 31

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.245 AC: 37135 AN: 151834 Hom.: 5253 Cov.: 31 AF XY: 0.236 AC XY: 17518 AN XY: 74222

African (AFR) AF: 0.388 AC: 16056 AN: 41386

American (AMR) AF: 0.212 AC: 3222 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3466

East Asian (EAS) AF: 0.138 AC: 709 AN: 5144

South Asian (SAS) AF: 0.101 AC: 486 AN: 4818

European-Finnish (FIN) AF: 0.102 AC: 1078 AN: 10582

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13981 AN: 67912

Other (OTH) AF: 0.264 AC: 557 AN: 2110

Alfa AF: 0.144 Hom.: 350

Bravo AF: 0.264

Asia WGS AF: 0.130 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.65
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs4700575; hg19: chr5-62595976;