rs304408

Variant names:

• chr18-1105248-T-C
• rs304408
• ENST00000577719.5:n.308-28595T>C

Variant summary

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

The ENST00000577719.5(ENSG00000263551):​n.308-28595T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,166 control chromosomes in the GnomAD database, including 2,909 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 0.18 (2909 hom., cov: 32)
• Consequence: ENSG00000263551 ENST00000577719.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 2 publications found

Genes affected

ENSG00000263551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577719.5. 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
	ENSG00000263551	ENST00000577719.5	TSL:3	n.308-28595T>C		intron	N/A
	ENSG00000263551	ENST00000579835.5	TSL:5	n.273-28595T>C		intron	N/A
	ENSG00000263551	ENST00000580781.5	TSL:3	n.307-28595T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28048 AN: 152048 Hom.: 2908 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.184 AC: 28057 AN: 152166 Hom.: 2909 Cov.: 32 AF XY: 0.188 AC XY: 14018 AN XY: 74378

African (AFR) AF: 0.164 AC: 6820 AN: 41524

American (AMR) AF: 0.164 AC: 2504 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2381 AN: 5164

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4820

European-Finnish (FIN) AF: 0.250 AC: 2644 AN: 10592

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11394 AN: 68002

Other (OTH) AF: 0.187 AC: 395 AN: 2110

Alfa AF: 0.172 Hom.: 1020

Bravo AF: 0.177

Asia WGS AF: 0.343 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.7
DANN	Benign	0.66
PhyloP100		0.30

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: rs304408;

hg19: chr18-1105249;