chr9-21707373-C-T

Position:

• chr9-21707373-C-T

Variant summary

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

The XR_001746563.3(LOC107987026):​n.164-4236G>A 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 0.601 in 151,510 control chromosomes in the GnomAD database, including 28,324 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 0.60 (28324 hom., cov: 30)
• Consequence: LOC107987026 XR_001746563.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

LOC107987026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987026	XR_001746563.3	n.164-4236G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91050 AN: 151412 Hom.: 28312 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.601 AC: 91101 AN: 151510 Hom.: 28324 Cov.: 30 AF XY: 0.597 AC XY: 44159 AN XY: 73996

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.588

Alfa AF: 0.525 Hom.: 9593

Bravo AF: 0.609

Asia WGS AF: 0.528 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	15
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: rs751173; hg19: chr9-21707372;