9-25501299-T-C

Variant names:

• chr9-25501299-T-C
• rs2210430
• XR_001746637.2:n.271-22934A>G

Variant summary

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

The XR_001746637.2(LOC107987056):​n.271-22934A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,212 control chromosomes in the GnomAD database, including 64,585 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 0.91 (64585 hom., cov: 33)
• Consequence: LOC107987056 XR_001746637.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 4 publications found

Genes affected

LOC107987056 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987056	XR_001746637.2	n.271-22934A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.914 AC: 139061 AN: 152094 Hom.: 64558 Cov.: 33

Gnomad AFR AF: 0.732

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.914 AC: 139140 AN: 152212 Hom.: 64585 Cov.: 33 AF XY: 0.916 AC XY: 68194 AN XY: 74436

African (AFR) AF: 0.732 AC: 30371 AN: 41486

American (AMR) AF: 0.958 AC: 14648 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3418 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5166 AN: 5166

South Asian (SAS) AF: 0.994 AC: 4800 AN: 4828

European-Finnish (FIN) AF: 0.978 AC: 10389 AN: 10620

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67181 AN: 68026

Other (OTH) AF: 0.933 AC: 1972 AN: 2114

Alfa AF: 0.886 Hom.: 4823

Bravo AF: 0.904

Asia WGS AF: 0.980 AC: 3406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.70
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2210430; hg19: chr9-25501297;