chr4-144559188-T-C

Variant names:

• chr4-144559188-T-C
• rs10519717
• ENST00000649263.1:n.328-143210A>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-143210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,116 control chromosomes in the GnomAD database, including 3,891 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 0.21 (3891 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 14 publications found

Genes affected

ENSG00000285713 (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 (SAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.164+2796A>G		intron_variant	Intron 1 of 7
LOC105377462	XR_939273.3	n.164+2796A>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-143210A>G		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-143210A>G		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32005 AN: 151998 Hom.: 3887 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.211 AC: 32041 AN: 152116 Hom.: 3891 Cov.: 32 AF XY: 0.212 AC XY: 15784 AN XY: 74390

African (AFR) AF: 0.286 AC: 11859 AN: 41492

American (AMR) AF: 0.290 AC: 4419 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1636 AN: 5172

South Asian (SAS) AF: 0.324 AC: 1559 AN: 4806

European-Finnish (FIN) AF: 0.112 AC: 1189 AN: 10604

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10156 AN: 67992

Other (OTH) AF: 0.213 AC: 449 AN: 2112

Alfa AF: 0.202 Hom.: 656

Bravo AF: 0.224

Asia WGS AF: 0.378 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10519717; hg19: chr4-145480340;