rs2157673

chr9-115796830-T-C

Variant summary

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

The XR_930269.2(LOC105376234):n.367-29755T>C 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 0.313 in 151,870 control chromosomes in the GnomAD database, including 7,529 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 (7529 hom., cov: 32)
• Consequence: LOC105376234 XR_930269.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

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 = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376234	XR_930269.2	n.367-29755T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47506 AN: 151750 Hom.: 7516 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.313 AC: 47547 AN: 151870 Hom.: 7529 Cov.: 32 AF XY: 0.315 AC XY: 23408 AN XY: 74242

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.321

Alfa AF: 0.321 Hom.: 13070

Bravo AF: 0.315

Asia WGS AF: 0.346 AC: 1201 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	2.8
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157673; hg19: chr9-118559109;