3-5847593-T-A

Variant names:

• chr3-5847593-T-A
• rs748192
• ENST00000425894.2:n.571+6350T>A

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.571+6350T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,094 control chromosomes in the GnomAD database, including 1,853 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 0.15 (1853 hom., cov: 31)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 3 publications found

Genes affected

ENSG00000229642 (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 (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425894.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229642	ENST00000425894.2	TSL:3	n.571+6350T>A		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.322+6350T>A		intron	N/A
	ENSG00000229642	ENST00000779002.1		n.342+6350T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22319 AN: 151978 Hom.: 1854 Cov.: 31

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.147 AC: 22329 AN: 152094 Hom.: 1853 Cov.: 31 AF XY: 0.148 AC XY: 11024 AN XY: 74354

African (AFR) AF: 0.0904 AC: 3753 AN: 41500

American (AMR) AF: 0.224 AC: 3430 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.139 AC: 718 AN: 5158

South Asian (SAS) AF: 0.112 AC: 539 AN: 4810

European-Finnish (FIN) AF: 0.165 AC: 1746 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10945 AN: 67972

Other (OTH) AF: 0.175 AC: 368 AN: 2106

Alfa AF: 0.149 Hom.: 187

Bravo AF: 0.149

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.48
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs748192; hg19: chr3-5889280;