9-119436925-A-T

Position:

• chr9-119436925-A-T

Variant summary

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

The XR_930305.2(LOC105376250):​n.189-5621T>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 0.601 in 152,040 control chromosomes in the GnomAD database, including 29,680 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 0.60 (29680 hom., cov: 32)
• Consequence: LOC105376250 XR_930305.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

Genes affected

LOC105376250 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376250	XR_930305.2	n.189-5621T>A		intron_variant, non_coding_transcript_variant
LOC105376250	XR_930304.2	n.189-5621T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91298 AN: 151924 Hom.: 29667 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.601 AC: 91328 AN: 152040 Hom.: 29680 Cov.: 32 AF XY: 0.603 AC XY: 44802 AN XY: 74286

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.609

Alfa AF: 0.651 Hom.: 4192

Bravo AF: 0.579

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1331623; hg19: chr9-122199203; COSMIC: COSV60399517;