9-5610381-C-T

Variant summary

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

The ENST00000661858.1(ENSG00000286162):n.182+19186G>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 0.311 in 151,966 control chromosomes in the GnomAD database, including 7,914 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 0.31 (7914 hom., cov: 32)
• Consequence: ENST00000661858.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902114	XR_007061406.1	n.161+19186G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661858.1	n.182+19186G>A		intron_variant, non_coding_transcript_variant
	ENST00000650674.2	n.226+18409G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47252 AN: 151848 Hom.: 7885 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.311 AC: 47318 AN: 151966 Hom.: 7914 Cov.: 32 AF XY: 0.316 AC XY: 23495 AN XY: 74256

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.298

Alfa AF: 0.291 Hom.: 13581

Bravo AF: 0.327

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.0
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4740820; hg19: chr9-5610381; COSMIC: COSV60324296;