rs1335510

Positions:

• chr9-21757804-T-G

Variant summary

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

The XR_001746563.3(LOC107987026):​n.163+10021A>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 0.323 in 151,982 control chromosomes in the GnomAD database, including 9,473 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 0.32 (9473 hom., cov: 32)
• Consequence: LOC107987026 XR_001746563.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

Genes affected

LOC107987026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987026	XR_001746563.3	n.163+10021A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49120 AN: 151864 Hom.: 9467 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.323 AC: 49143 AN: 151982 Hom.: 9473 Cov.: 32 AF XY: 0.323 AC XY: 23986 AN XY: 74250

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.332

Alfa AF: 0.389 Hom.: 6135

Bravo AF: 0.315

Asia WGS AF: 0.317 AC: 1099 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1335510; hg19: chr9-21757803;