rs2352904

Positions:

• chr14-48903598-A-C
• chr14-48903598-A-G
• chr14-48903598-A-T

Variant summary

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

The XR_007064152.1(LOC105378178):​n.345+166194T>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 0.557 in 151,358 control chromosomes in the GnomAD database, including 23,771 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 (23771 hom., cov: 30)
• Consequence: LOC105378178 XR_007064152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

LOC105378178 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378178	XR_007064152.1	n.345+166194T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84275 AN: 151242 Hom.: 23738 Cov.: 30

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.557 AC: 84358 AN: 151358 Hom.: 23771 Cov.: 30 AF XY: 0.555 AC XY: 41045 AN XY: 73902

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.545

Alfa AF: 0.571 Hom.: 44746

Bravo AF: 0.555

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2352904; hg19: chr14-49372801;