5-4201618-G-T

Variant names:

• chr5-4201618-G-T
• rs6555263

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 0.901 in 151,822 control chromosomes in the GnomAD database, including 62,235 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 0.90 (62235 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.901 AC: 136739 AN: 151704 Hom.: 62217 Cov.: 30

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.901 AC: 136804 AN: 151822 Hom.: 62235 Cov.: 30 AF XY: 0.903 AC XY: 67009 AN XY: 74186

African (AFR) AF: 0.764 AC: 31523 AN: 41250

American (AMR) AF: 0.941 AC: 14378 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3203 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5124 AN: 5154

South Asian (SAS) AF: 0.890 AC: 4282 AN: 4810

European-Finnish (FIN) AF: 0.985 AC: 10399 AN: 10560

Middle Eastern (MID) AF: 0.935 AC: 273 AN: 292

European-Non Finnish (NFE) AF: 0.954 AC: 64859 AN: 67988

Other (OTH) AF: 0.894 AC: 1888 AN: 2112

Alfa AF: 0.924 Hom.: 10434

Bravo AF: 0.893

Asia WGS AF: 0.893 AC: 3097 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6555263; hg19: chr5-4201731;