chr9-37368456-C-G

Variant names:

• chr9-37368456-C-G
• rs308516
• XR_007061478.1:n.4375+1854C>G

Variant summary

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

The XR_007061478.1(LOC124902153):​n.4375+1854C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 149,572 control chromosomes in the GnomAD database, including 174 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 0.032 (174 hom., cov: 31)
• Consequence: LOC124902153 XR_007061478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 1 publications found

Genes affected

LOC124902153 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902153	XR_007061478.1	n.4375+1854C>G		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0316 AC: 4723 AN: 149458 Hom.: 173 Cov.: 31

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.0716

Gnomad FIN AF: 0.00555

Gnomad MID AF: 0.0329

Gnomad NFE AF: 0.00316

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0316 AC: 4732 AN: 149572 Hom.: 174 Cov.: 31 AF XY: 0.0333 AC XY: 2426 AN XY: 72834

African (AFR) AF: 0.0801 AC: 3242 AN: 40492

American (AMR) AF: 0.0186 AC: 278 AN: 14940

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3462

East Asian (EAS) AF: 0.0744 AC: 376 AN: 5052

South Asian (SAS) AF: 0.0722 AC: 341 AN: 4724

European-Finnish (FIN) AF: 0.00555 AC: 55 AN: 9916

Middle Eastern (MID) AF: 0.0355 AC: 10 AN: 282

European-Non Finnish (NFE) AF: 0.00316 AC: 214 AN: 67718

Other (OTH) AF: 0.0303 AC: 63 AN: 2076

Alfa AF: 0.00494 Hom.: 2

Bravo AF: 0.0329

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs308516; hg19: chr9-37368453;