5-104690006-C-T

Variant names:

• chr5-104690006-C-T
• rs428538
• ENST00000503650.1:n.328+196852G>A

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.328+196852G>A variant causes a intron 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: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 3 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105379109	NR_188304.1	n.176-51479G>A		intron_variant	Intron 2 of 3
LOC105379109	NR_188305.1	n.296-51479G>A		intron_variant	Intron 2 of 3
LOC105379109	NR_188306.1	n.176-59350G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251574	ENST00000503650.1	n.328+196852G>A		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000505824.6	n.308-59350G>A		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000506976.6	n.204-51479G>A		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.480 AC: 19546 AN: 40702

American (AMR) AF: 0.389 AC: 5815 AN: 14938

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3466

East Asian (EAS) AF: 0.0504 AC: 258 AN: 5122

South Asian (SAS) AF: 0.283 AC: 1357 AN: 4798

European-Finnish (FIN) AF: 0.295 AC: 3005 AN: 10202

Middle Eastern (MID) AF: 0.359 AC: 104 AN: 290

European-Non Finnish (NFE) AF: 0.325 AC: 22052 AN: 67884

Other (OTH) AF: 0.345 AC: 723 AN: 2096

Alfa AF: 0.352 Hom.: 11376

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs428538; hg19: chr5-104025707;