rs1332408

chr9-122429880-C-Achr9-122429880-C-T

Variant summary

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

The ENST00000431442.2(ENSG00000234156):n.323+12995C>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 0.247 in 152,004 control chromosomes in the GnomAD database, including 4,648 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 0.25 (4648 hom., cov: 32)
• Consequence: ENST00000431442.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000431442.2	n.323+12995C>A		intron_variant, non_coding_transcript_variant		3
	ENST00000433572.3	n.357+12995C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37443 AN: 151886 Hom.: 4643 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.247 AC: 37475 AN: 152004 Hom.: 4648 Cov.: 32 AF XY: 0.249 AC XY: 18497 AN XY: 74286

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.250

Alfa AF: 0.234 Hom.: 8763

Bravo AF: 0.249

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.1
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1332408; hg19: chr9-125192159;