rs1902498

Positions:

• chr4-154995423-C-T

Variant summary

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

The variant allele was found at a frequency of 0.514 in 152,034 control chromosomes in the GnomAD database, including 23,746 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 0.51 (23746 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.154995423C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78048 AN: 151916 Hom.: 23688 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.514 AC: 78151 AN: 152034 Hom.: 23746 Cov.: 32 AF XY: 0.514 AC XY: 38205 AN XY: 74336

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.483

Alfa AF: 0.401 Hom.: 6514

Bravo AF: 0.526

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1902498; hg19: chr4-155916575;