rs17019336

Variant names:

• chr4-144412457-T-A
• rs17019336
• ENST00000649263.1:n.*43+3446A>T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.*43+3446A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,142 control chromosomes in the GnomAD database, including 3,153 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 0.18 (3153 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 9 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.314+3446A>T		intron_variant	Intron 3 of 7
LOC105377462	XR_939273.3	n.240+3446A>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.*43+3446A>T		intron_variant	Intron 5 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000648340.1	n.214+3446A>T		intron_variant	Intron 2 of 5
ENSG00000285783	ENST00000650526.1	n.298+3446A>T		intron_variant	Intron 3 of 14

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27399 AN: 152024 Hom.: 3156 Cov.: 32

Gnomad AFR AF: 0.0436

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.180 AC: 27393 AN: 152142 Hom.: 3153 Cov.: 32 AF XY: 0.180 AC XY: 13368 AN XY: 74392

African (AFR) AF: 0.0435 AC: 1806 AN: 41552

American (AMR) AF: 0.213 AC: 3259 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3468

East Asian (EAS) AF: 0.328 AC: 1687 AN: 5144

South Asian (SAS) AF: 0.0879 AC: 424 AN: 4824

European-Finnish (FIN) AF: 0.218 AC: 2311 AN: 10602

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16381 AN: 67964

Other (OTH) AF: 0.208 AC: 440 AN: 2114

Alfa AF: 0.199 Hom.: 428

Bravo AF: 0.180

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.4
DANN	Benign	0.74
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs17019336; hg19: chr4-145333609;