9-79463998-T-A

Position:

• chr9-79463998-T-A

Variant summary

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

The XR_007061902.1(LOC124902328):​n.84-3996A>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 0.127 in 152,156 control chromosomes in the GnomAD database, including 1,319 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 0.13 (1319 hom., cov: 33)
• Consequence: LOC124902328 XR_007061902.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

Genes affected

LOC124902328 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902328	XR_007061902.1	n.84-3996A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19225 AN: 152038 Hom.: 1308 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.127 AC: 19265 AN: 152156 Hom.: 1319 Cov.: 33 AF XY: 0.131 AC XY: 9721 AN XY: 74388

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0987

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.116

Alfa AF: 0.122 Hom.: 145

Bravo AF: 0.126

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7044969; hg19: chr9-82078913;