rs4955755

Positions:

• chr3-170776620-G-A
• chr3-170776620-G-C
• chr3-170776620-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000486975.1(ENSG00000285218):​c.*44+68426G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,022 control chromosomes in the GnomAD database, including 26,200 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 0.56 (26200 hom., cov: 33)
• Consequence: ENSG00000285218 ENST00000486975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

ENSG00000285218 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374211	XR_924701.2	n.1210+4553G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285218	ENST00000486975.1	c.*44+68426G>A		intron_variant		2		ENSP00000417434.1
SLC7A14-AS1	ENST00000644993.1	n.293+68426G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84561 AN: 151904 Hom.: 26197 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.556 AC: 84574 AN: 152022 Hom.: 26200 Cov.: 33 AF XY: 0.553 AC XY: 41108 AN XY: 74312

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.571

Alfa AF: 0.676 Hom.: 80355

Bravo AF: 0.537

Asia WGS AF: 0.477 AC: 1654 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	14
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4955755; hg19: chr3-170494409;