9-104932241-C-T

Position:

• chr9-104932241-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_930204.3(LOC105376196):​n.1339+2517C>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 0.188 in 152,084 control chromosomes in the GnomAD database, including 3,266 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3266 hom., cov: 31)
• Consequence: LOC105376196 XR_930204.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

Genes affected

LOC105376196 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376196	XR_930204.3	n.1339+2517C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28571 AN: 151966 Hom.: 3272 Cov.: 31

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.188 AC: 28571 AN: 152084 Hom.: 3266 Cov.: 31 AF XY: 0.193 AC XY: 14365 AN XY: 74340

Gnomad4 AFR AF: 0.0610

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.190

Alfa AF: 0.198 Hom.: 436

Bravo AF: 0.175

Asia WGS AF: 0.300 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.060
CADD	Benign	18
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2487042; hg19: chr9-107694522;