rs999924

Positions:

• chr9-1332257-G-A
• chr9-1332257-G-C
• chr9-1332257-G-T

Variant summary

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

The XR_002956872.2(LOC102723803):​n.356+21225G>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 0.357 in 151,972 control chromosomes in the GnomAD database, including 10,491 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 0.36 (10491 hom., cov: 32)
• Consequence: LOC102723803 XR_002956872.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

LOC102723803 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723803	XR_002956872.2	n.356+21225G>A		intron_variant, non_coding_transcript_variant
LOC102723803	XR_428436.4	n.620-890G>A		intron_variant, non_coding_transcript_variant
LOC102723803	XR_929415.3	n.356+21225G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54256 AN: 151854 Hom.: 10469 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.357 AC: 54308 AN: 151972 Hom.: 10491 Cov.: 32 AF XY: 0.369 AC XY: 27379 AN XY: 74298

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.336

Alfa AF: 0.289 Hom.: 6925

Bravo AF: 0.359

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999924; hg19: chr9-1332257;