rs7614488

Positions:

• chr3-106302653-T-C

Variant summary

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

The XR_001740840.1(LOC107986112):​n.82+1537A>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 0.811 in 151,976 control chromosomes in the GnomAD database, including 52,015 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 0.81 (52015 hom., cov: 31)
• Consequence: LOC107986112 XR_001740840.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

Genes affected

LOC107986112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986112	XR_001740840.1	n.82+1537A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123234 AN: 151860 Hom.: 51995 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.811 AC: 123296 AN: 151976 Hom.: 52015 Cov.: 31 AF XY: 0.811 AC XY: 60256 AN XY: 74288

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.830

Alfa AF: 0.913 Hom.: 129289

Bravo AF: 0.793

Asia WGS AF: 0.805 AC: 2798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7614488; hg19: chr3-106021500;