rs9310784

chr3-25888713-T-C

Variant summary

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

The XR_007095849.1(LOC124909357):n.226+14710T>C 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 0.201 in 152,136 control chromosomes in the GnomAD database, including 3,718 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 0.20 (3718 hom., cov: 32)
• Consequence: LOC124909357 XR_007095849.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

LOC124909357 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909357	XR_007095849.1	n.226+14710T>C		intron_variant, non_coding_transcript_variant
LOC124909357	XR_007095848.1	n.123+14813T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30557 AN: 152018 Hom.: 3714 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.201 AC: 30578 AN: 152136 Hom.: 3718 Cov.: 32 AF XY: 0.200 AC XY: 14841 AN XY: 74390

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.175

Alfa AF: 0.164 Hom.: 1299

Bravo AF: 0.205

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.0
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9310784; hg19: chr3-25930204;