ENST00000577719.5:n.308-27502C>T

Variant names:

• chr18-1106341-C-T
• rs304409
• ENST00000577719.5:n.308-27502C>T

Variant summary

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

The ENST00000577719.5(ENSG00000263551):​n.308-27502C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,958 control chromosomes in the GnomAD database, including 12,379 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 0.35 (12379 hom., cov: 31)
• Consequence: ENSG00000263551 ENST00000577719.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371953	XR_001753318.2	n.343+6994C>T		intron_variant	Intron 1 of 6
LOC105371953	XR_007066436.1	n.343+6994C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263551	ENST00000577719.5	n.308-27502C>T		intron_variant	Intron 1 of 3	3
ENSG00000263551	ENST00000579835.5	n.273-27502C>T		intron_variant	Intron 2 of 4	5
ENSG00000263551	ENST00000580781.5	n.307-27502C>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53654 AN: 151838 Hom.: 12341 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.354 AC: 53740 AN: 151958 Hom.: 12379 Cov.: 31 AF XY: 0.353 AC XY: 26177 AN XY: 74244

African (AFR) AF: 0.653 AC: 27039 AN: 41436

American (AMR) AF: 0.237 AC: 3615 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2385 AN: 5158

South Asian (SAS) AF: 0.302 AC: 1453 AN: 4806

European-Finnish (FIN) AF: 0.292 AC: 3073 AN: 10538

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14519 AN: 67950

Other (OTH) AF: 0.319 AC: 674 AN: 2110

Alfa AF: 0.270 Hom.: 12955

Bravo AF: 0.362

Asia WGS AF: 0.405 AC: 1407 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.20
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs304409; hg19: chr18-1106342;