rs4549225

Positions:

• chr3-66717035-A-G
• chr3-66717035-A-T

Variant summary

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

The XR_940935.3(LOC105377142):​n.185+909T>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 0.66 in 152,120 control chromosomes in the GnomAD database, including 34,390 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 0.66 (34390 hom., cov: 33)
• Consequence: LOC105377142 XR_940935.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

Genes affected

LOC105377142 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377142	XR_940935.3	n.185+909T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100371 AN: 152000 Hom.: 34349 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.660 AC: 100462 AN: 152120 Hom.: 34390 Cov.: 33 AF XY: 0.658 AC XY: 48949 AN XY: 74358

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.652

Alfa AF: 0.630 Hom.: 4916

Bravo AF: 0.673

Asia WGS AF: 0.531 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4549225; hg19: chr3-66767459;