9-37376125-A-T

Position:

• chr9-37376125-A-T

Variant summary

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

The XR_007061478.1(LOC124902153):​n.4376-6052A>T 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 0.235 in 150,350 control chromosomes in the GnomAD database, including 4,440 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 0.24 (4440 hom., cov: 29)
• Consequence: LOC124902153 XR_007061478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

LOC124902153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902153	XR_007061478.1	n.4376-6052A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35317 AN: 150240 Hom.: 4436 Cov.: 29

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.235 AC: 35336 AN: 150350 Hom.: 4440 Cov.: 29 AF XY: 0.230 AC XY: 16828 AN XY: 73322

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.264

Alfa AF: 0.0978 Hom.: 144

Bravo AF: 0.239

Asia WGS AF: 0.159 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.32
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: rs7031314; hg19: chr9-37376122;