rs999924

Variant names:

• chr9-1332257-G-A
• rs999924
• ENST00000822116.1:n.573-890G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000822116.1(ENSG00000306944):​n.573-890G>A variant causes a intron 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: ENSG00000306944 ENST00000822116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 4 publications found

Genes affected

ENSG00000306944 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC102723803	XR_002956872.2	n.356+21225G>A		intron_variant	Intron 3 of 7
LOC102723803	XR_428436.4	n.620-890G>A		intron_variant	Intron 5 of 5
LOC102723803	XR_929415.3	n.356+21225G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306944	ENST00000822116.1	n.573-890G>A		intron_variant	Intron 5 of 6
ENSG00000306944	ENST00000822117.1	n.404-890G>A		intron_variant	Intron 4 of 5
ENSG00000306944	ENST00000822118.1	n.359-890G>A		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.393 AC: 16289 AN: 41430

American (AMR) AF: 0.441 AC: 6730 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3383 AN: 5178

South Asian (SAS) AF: 0.383 AC: 1845 AN: 4822

European-Finnish (FIN) AF: 0.445 AC: 4693 AN: 10542

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19093 AN: 67948

Other (OTH) AF: 0.336 AC: 707 AN: 2106

Alfa AF: 0.298 Hom.: 9620

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
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs999924; hg19: chr9-1332257;