rs1905339

Variant names:

• chr17-42430278-T-C
• rs1905339
• ENST00000723360.1:n.821+5216T>C

Variant summary

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

The ENST00000723360.1(ENSG00000294400):​n.821+5216T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,992 control chromosomes in the GnomAD database, including 8,205 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 0.32 (8205 hom., cov: 31)
• Consequence: ENSG00000294400 ENST00000723360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711
• Publications: 19 publications found

Genes affected

ENSG00000294400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723360.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294400	ENST00000723360.1		n.821+5216T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49058 AN: 151874 Hom.: 8188 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.323 AC: 49115 AN: 151992 Hom.: 8205 Cov.: 31 AF XY: 0.325 AC XY: 24165 AN XY: 74250

African (AFR) AF: 0.323 AC: 13369 AN: 41452

American (AMR) AF: 0.261 AC: 3989 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3472

East Asian (EAS) AF: 0.358 AC: 1850 AN: 5170

South Asian (SAS) AF: 0.499 AC: 2403 AN: 4816

European-Finnish (FIN) AF: 0.329 AC: 3467 AN: 10550

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21991 AN: 67958

Other (OTH) AF: 0.347 AC: 733 AN: 2110

Alfa AF: 0.326 Hom.: 34613

Bravo AF: 0.314

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.9
DANN	Benign	0.71
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs1905339; hg19: chr17-40582296;