rs308516

Positions:

• chr9-37368456-C-G
• chr9-37368456-C-T

Variant summary

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

The XR_007061478.1(LOC124902153):​n.4375+1854C>G 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 0.0316 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880

Genes affected

LOC124902153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124902153	XR_007061478.1	n.4375+1854C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.0186

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.0744

Gnomad4 SAS AF: 0.0722

Gnomad4 FIN AF: 0.00555

Gnomad4 NFE AF: 0.00316

Gnomad4 OTH AF: 0.0303

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs308516; hg19: chr9-37368453;