rs2270851

chr4-22329842-A-C

Variant summary

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

The ENST00000510705.3(ENSG00000250039):n.1386A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,878 control chromosomes in the GnomAD database, including 3,994 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 0.22 (3994 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENST00000510705.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100505912	NR_037877.1	n.362+15T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000510705.3	n.1386A>C		non_coding_transcript_exon_variant	4/4	5

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34057 AN: 151756 Hom.: 3992 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.224 AC: 34080 AN: 151876 Hom.: 3994 Cov.: 31 AF XY: 0.227 AC XY: 16850 AN XY: 74222

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.243

Alfa AF: 0.213 Hom.: 1667

Bravo AF: 0.233

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.13
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2270851; hg19: chr4-22331465;