rs2851024

Variant names:

• chr4-99469947-A-C
• rs2851024
• ENST00000506494.1:n.440-131T>G

Variant summary

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

The ENST00000506494.1(ENSG00000250300):​n.440-131T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,054 control chromosomes in the GnomAD database, including 11,092 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 (11091 hom., cov: 32)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: ENSG00000250300 ENST00000506494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

ENSG00000250300 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 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
ENSG00000250300	ENST00000506494.1	n.440-131T>G		intron_variant	Intron 3 of 3	6

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55428 AN: 151928 Hom.: 11086 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.347

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.365 AC: 55472 AN: 152048 Hom.: 11091 Cov.: 32 AF XY: 0.366 AC XY: 27182 AN XY: 74340

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.346

Alfa AF: 0.423 Hom.: 18655

Bravo AF: 0.356

Asia WGS AF: 0.340 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
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: rs2851024; hg19: chr4-100391104;