18-24766177-C-T

Variant names:

• chr18-24766177-C-T
• rs7229673
• ENST00000577354.6:n.308-304C>T

Variant summary

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

The ENST00000577354.6(ENSG00000266573):​n.308-304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,098 control chromosomes in the GnomAD database, including 3,961 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 0.23 (3961 hom., cov: 33)
• Consequence: ENSG00000266573 ENST00000577354.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 1 publications found

Genes affected

ENSG00000266573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372028	NR_134604.1	n.308-304C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266573	ENST00000577354.6	n.308-304C>T		intron_variant	Intron 2 of 3	4
ENSG00000266573	ENST00000582650.5	n.235+39420C>T		intron_variant	Intron 2 of 3	4
ENSG00000266573	ENST00000654065.1	n.226+39420C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34374 AN: 151978 Hom.: 3965 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.226 AC: 34380 AN: 152098 Hom.: 3961 Cov.: 33 AF XY: 0.227 AC XY: 16903 AN XY: 74344

African (AFR) AF: 0.231 AC: 9581 AN: 41462

American (AMR) AF: 0.195 AC: 2983 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1104 AN: 5180

South Asian (SAS) AF: 0.240 AC: 1161 AN: 4832

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10572

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15278 AN: 67994

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.215 Hom.: 509

Bravo AF: 0.221

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.20
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs7229673; hg19: chr18-22346141;