5-75785095-G-T

Variant names:

• chr5-75785095-G-T
• rs258506
• ENST00000814440.1:n.438-17886G>T

Variant summary

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

The ENST00000814440.1(ENSG00000305970):​n.438-17886G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,872 control chromosomes in the GnomAD database, including 7,588 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 0.30 (7588 hom., cov: 32)
• Consequence: ENSG00000305970 ENST00000814440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 1 publications found

Genes affected

ENSG00000305970 (HGNC:59071):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814440.1. 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
	ENSG00000305970	ENST00000814440.1		n.438-17886G>T		intron	N/A
	ENSG00000305970	ENST00000814441.1		n.438-17886G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45670 AN: 151754 Hom.: 7584 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.301 AC: 45692 AN: 151872 Hom.: 7588 Cov.: 32 AF XY: 0.304 AC XY: 22546 AN XY: 74234

African (AFR) AF: 0.159 AC: 6597 AN: 41464

American (AMR) AF: 0.285 AC: 4345 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3466

East Asian (EAS) AF: 0.496 AC: 2561 AN: 5162

South Asian (SAS) AF: 0.298 AC: 1437 AN: 4822

European-Finnish (FIN) AF: 0.389 AC: 4099 AN: 10532

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24648 AN: 67886

Other (OTH) AF: 0.300 AC: 634 AN: 2116

Alfa AF: 0.205 Hom.: 522

Bravo AF: 0.286

Asia WGS AF: 0.359 AC: 1243 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.23
PhyloP100		-2.0

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: rs258506;

hg19: chr5-75080920;