rs2422493

Positions:

• chr9-104928714-G-A

Variant summary

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

The ENST00000435915.1(ENSG00000226334):​n.359-68G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,904 control chromosomes in the GnomAD database, including 17,594 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 0.48 (17590 hom., cov: 31)
  • Exomes 𝑓: 0.50 (4 hom.)
• Consequence: ENST00000435915.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376196	XR_930204.3	n.1123-794G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435915.1	n.359-68G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72587 AN: 151754 Hom.: 17584 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 0.500 AC: 16 AN: 32 Hom.: 4 AF XY: 0.464 AC XY: 13 AN XY: 28

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.478 AC: 72625 AN: 151872 Hom.: 17590 Cov.: 31 AF XY: 0.483 AC XY: 35868 AN XY: 74226

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.484

Alfa AF: 0.474 Hom.: 14842

Bravo AF: 0.474

Asia WGS AF: 0.479 AC: 1662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2422493; hg19: chr9-107690995;