9-23664509-C-T

Position:

• chr9-23664509-C-T

Variant summary

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

The NR_121602.1(LOC101929563):​n.445-1492G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.70 (31695 hom., cov: 20)
• Consequence: LOC101929563 NR_121602.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929563	NR_121602.1	n.445-1492G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000640307.1	n.433-1492G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.695 AC: 93977 AN: 135232 Hom.: 31678 Cov.: 20

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.695 AC: 94010 AN: 135264 Hom.: 31695 Cov.: 20 AF XY: 0.699 AC XY: 45429 AN XY: 64994

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.687

Alfa AF: 0.656 Hom.: 2439

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2116226; hg19: chr9-23664507;