5-4201651-G-C

Variant names:

• chr5-4201651-G-C
• rs6555264

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 0.91 in 151,556 control chromosomes in the GnomAD database, including 63,189 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 0.91 (63189 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.910 AC: 137855 AN: 151442 Hom.: 63170 Cov.: 28

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.910 AC: 137919 AN: 151556 Hom.: 63189 Cov.: 28 AF XY: 0.912 AC XY: 67529 AN XY: 74054

African (AFR) AF: 0.795 AC: 32692 AN: 41120

American (AMR) AF: 0.944 AC: 14398 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3201 AN: 3466

East Asian (EAS) AF: 0.994 AC: 5093 AN: 5122

South Asian (SAS) AF: 0.894 AC: 4292 AN: 4802

European-Finnish (FIN) AF: 0.985 AC: 10369 AN: 10530

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

European-Non Finnish (NFE) AF: 0.954 AC: 64835 AN: 67952

Other (OTH) AF: 0.901 AC: 1893 AN: 2102

Alfa AF: 0.932 Hom.: 8246

Bravo AF: 0.903

Asia WGS AF: 0.896 AC: 3109 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.55
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6555264; hg19: chr5-4201764;