rs428538

chr5-104690006-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503650.1(ENSG00000251574):n.328+196852G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 150,406 control chromosomes in the GnomAD database, including 10,570 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 0.36 (10570 hom., cov: 29)
• Consequence: ENST00000503650.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379109	XR_948647.2	n.324-59350G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000503650.1	n.328+196852G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54218 AN: 150288 Hom.: 10545 Cov.: 29

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.361 AC: 54286 AN: 150406 Hom.: 10570 Cov.: 29 AF XY: 0.359 AC XY: 26307 AN XY: 73314

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.0504

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.345

Alfa AF: 0.332 Hom.: 5852

Bravo AF: 0.375

Asia WGS AF: 0.206 AC: 717 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs428538; hg19: chr5-104025707;