rs4440084

Positions:

• chr3-166114553-C-G
• chr3-166114553-C-T

Variant summary

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

The XR_007096287.1(LOC124909497):​n.36+12990C>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 0.593 in 151,592 control chromosomes in the GnomAD database, including 27,934 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 0.59 (27934 hom., cov: 30)
• Consequence: LOC124909497 XR_007096287.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

Genes affected

LOC124909497 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124909497	XR_007096287.1	n.36+12990C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89798 AN: 151472 Hom.: 27898 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.593 AC: 89879 AN: 151592 Hom.: 27934 Cov.: 30 AF XY: 0.591 AC XY: 43732 AN XY: 74026

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.588

Alfa AF: 0.461 Hom.: 1377

Bravo AF: 0.603

Asia WGS AF: 0.468 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.3
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: rs4440084; hg19: chr3-165832341;