5-4197559-A-G

Variant names:

• chr5-4197559-A-G
• rs6555254
• ENST00000762810.1:n.547-510A>G

Variant summary

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

The ENST00000762810.1(ENSG00000299354):​n.547-510A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,054 control chromosomes in the GnomAD database, including 67,472 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 0.94 (67472 hom., cov: 29)
• Consequence: ENSG00000299354 ENST00000762810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 3 publications found

Genes affected

ENSG00000299354 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762810.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299354	ENST00000762810.1		n.547-510A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143038 AN: 151936 Hom.: 67437 Cov.: 29

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.941 AC: 143125 AN: 152054 Hom.: 67472 Cov.: 29 AF XY: 0.942 AC XY: 70026 AN XY: 74324

African (AFR) AF: 0.895 AC: 37073 AN: 41444

American (AMR) AF: 0.961 AC: 14682 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3361 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5128 AN: 5158

South Asian (SAS) AF: 0.906 AC: 4347 AN: 4796

European-Finnish (FIN) AF: 0.985 AC: 10424 AN: 10586

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 64988 AN: 68002

Other (OTH) AF: 0.933 AC: 1968 AN: 2110

Alfa AF: 0.949 Hom.: 8338

Bravo AF: 0.940

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.069
DANN	Benign	0.44
PhyloP100		0.074

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6555254;

hg19: chr5-4197672;