rs4835180

Variant names:

• chr4-144599456-A-G
• rs4835180
• ENST00000649263.1:n.328-183478T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-183478T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,078 control chromosomes in the GnomAD database, including 15,496 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 0.43 (15496 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-183478T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+155701T>C		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.434 AC: 66000 AN: 151960 Hom.: 15485 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.434 AC: 66060 AN: 152078 Hom.: 15496 Cov.: 32 AF XY: 0.444 AC XY: 33026 AN XY: 74336

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.434

Alfa AF: 0.480 Hom.: 23197

Bravo AF: 0.421

Asia WGS AF: 0.580 AC: 2004 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4835180; hg19: chr4-145520608;