8-27595505-C-T

Variant names:

• chr8-27595505-C-T
• rs17057441
• ENST00000774582.1:n.518C>T

Variant summary

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

The ENST00000774582.1(ENSG00000300853):​n.518C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0373 in 152,258 control chromosomes in the GnomAD database, including 124 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 0.037 (124 hom., cov: 32)
• Consequence: ENSG00000300853 ENST00000774582.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 3 publications found

Genes affected

ENSG00000300853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901919	XR_007060868.1	n.1398-1562C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300853	ENST00000774582.1	n.518C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000300853	ENST00000774578.1	n.170-1562C>T		intron_variant	Intron 1 of 1
ENSG00000300853	ENST00000774579.1	n.285-1562C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0373 AC: 5674 AN: 152140 Hom.: 124 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0633

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0442

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

GnomAD4 genome AF: 0.0373 AC: 5679 AN: 152258 Hom.: 124 Cov.: 32 AF XY: 0.0360 AC XY: 2677 AN XY: 74454

African (AFR) AF: 0.0666 AC: 2765 AN: 41526

American (AMR) AF: 0.0256 AC: 392 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0629 AC: 303 AN: 4816

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10618

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0283 AC: 1923 AN: 68018

Other (OTH) AF: 0.0433 AC: 91 AN: 2104

Alfa AF: 0.0302 Hom.: 131

Bravo AF: 0.0384

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.62
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs17057441; hg19: chr8-27453022;