rs978724

Positions:

• chr9-115760700-G-T

Variant summary

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

The XR_930269.2(LOC105376234):​n.366+12974G>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 0.0154 in 152,026 control chromosomes in the GnomAD database, including 48 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 0.015 (48 hom., cov: 32)
• Consequence: LOC105376234 XR_930269.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

Genes affected

LOC105376234 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376234	XR_930269.2	n.366+12974G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0154 AC: 2342 AN: 151908 Hom.: 48 Cov.: 32

Gnomad AFR AF: 0.00317

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.0894

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.00490

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0152

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0154 AC: 2341 AN: 152026 Hom.: 48 Cov.: 32 AF XY: 0.0166 AC XY: 1230 AN XY: 74286

Gnomad4 AFR AF: 0.00316

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.0892

Gnomad4 SAS AF: 0.0609

Gnomad4 FIN AF: 0.00490

Gnomad4 NFE AF: 0.0152

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.0151 Hom.: 5

Bravo AF: 0.0153

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.60
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs978724; hg19: chr9-118522979;