rs569945

chr4-178146507-G-Achr4-178146507-G-C

Variant summary

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

The XR_939514.1(LOC105377562):n.645-3231G>A 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 0.611 in 151,862 control chromosomes in the GnomAD database, including 28,559 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 0.61 (28559 hom., cov: 33)
• Consequence: LOC105377562 XR_939514.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

LOC105377562 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377562	XR_939514.1	n.645-3231G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92711 AN: 151746 Hom.: 28534 Cov.: 33

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.611 AC: 92788 AN: 151862 Hom.: 28559 Cov.: 33 AF XY: 0.613 AC XY: 45512 AN XY: 74214

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.665

Alfa AF: 0.616 Hom.: 13037

Bravo AF: 0.611

Asia WGS AF: 0.658 AC: 2286 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.019
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs569945; hg19: chr4-179067661;