rs28542567

Variant names:

• chr4-4931095-G-A
• rs28542567
• ENST00000774609.1:n.142-2725G>A

Variant summary

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

The ENST00000774609.1(ENSG00000300857):​n.142-2725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0473 in 152,120 control chromosomes in the GnomAD database, including 240 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 0.047 (240 hom., cov: 33)
• Consequence: ENSG00000300857 ENST00000774609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 1 publications found

Genes affected

ENSG00000300857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928306	NR_125893.1	n.354-2725G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300857	ENST00000774609.1	n.142-2725G>A		intron_variant	Intron 2 of 8
ENSG00000300857	ENST00000774610.1	n.165-2725G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 7196 AN: 152004 Hom.: 239 Cov.: 33

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0370

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0659

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0473 AC: 7192 AN: 152120 Hom.: 240 Cov.: 33 AF XY: 0.0462 AC XY: 3433 AN XY: 74350

African (AFR) AF: 0.0103 AC: 426 AN: 41510

American (AMR) AF: 0.0370 AC: 565 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3466

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5174

South Asian (SAS) AF: 0.116 AC: 559 AN: 4800

European-Finnish (FIN) AF: 0.0397 AC: 420 AN: 10568

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0659 AC: 4482 AN: 67996

Other (OTH) AF: 0.0492 AC: 104 AN: 2112

Alfa AF: 0.0581 Hom.: 36

Bravo AF: 0.0430

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.40
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs28542567; hg19: chr4-4932822;