rs5008499

Variant names:

• chr6-18044947-C-T
• rs5008499
• ENST00000747204.1:n.89-10738C>T

Variant summary

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

The ENST00000747204.1(ENSG00000297344):​n.89-10738C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,154 control chromosomes in the GnomAD database, including 2,348 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 0.16 (2348 hom., cov: 32)
• Consequence: ENSG00000297344 ENST00000747204.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 5 publications found

Genes affected

ENSG00000297344 (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 (AMR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747204.1. 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
	ENSG00000297344	ENST00000747204.1		n.89-10738C>T		intron	N/A
	ENSG00000297344	ENST00000747205.1		n.178+1521C>T		intron	N/A
	ENSG00000297358	ENST00000747318.1		n.227+6807G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25044 AN: 152036 Hom.: 2339 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.165 AC: 25077 AN: 152154 Hom.: 2348 Cov.: 32 AF XY: 0.169 AC XY: 12556 AN XY: 74394

African (AFR) AF: 0.110 AC: 4574 AN: 41518

American (AMR) AF: 0.278 AC: 4241 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3468

East Asian (EAS) AF: 0.167 AC: 862 AN: 5172

South Asian (SAS) AF: 0.176 AC: 850 AN: 4820

European-Finnish (FIN) AF: 0.193 AC: 2044 AN: 10588

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11367 AN: 67994

Other (OTH) AF: 0.174 AC: 368 AN: 2114

Alfa AF: 0.168 Hom.: 6205

Bravo AF: 0.169

Asia WGS AF: 0.175 AC: 608 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	1.0
DANN	Benign	0.24
PhyloP100		-0.15

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: rs5008499;

hg19: chr6-18045178;