rs815703

chr3-61287099-T-A

Variant summary

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

The XR_001740725.2(LOC105377114):n.708-2435A>T 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 0.149 in 152,154 control chromosomes in the GnomAD database, including 1,783 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 0.15 (1783 hom., cov: 32)
• Consequence: LOC105377114 XR_001740725.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

Genes affected

LOC105377114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377114	XR_001740725.2	n.708-2435A>T		intron_variant, non_coding_transcript_variant
LOC105377114	XR_940892.3	n.822-2435A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22685 AN: 152036 Hom.: 1781 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.149 AC: 22694 AN: 152154 Hom.: 1783 Cov.: 32 AF XY: 0.149 AC XY: 11078 AN XY: 74380

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0651

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.157

Alfa AF: 0.157 Hom.: 239

Bravo AF: 0.151

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	1.9
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs815703; hg19: chr3-61272773;