chr4-114717445-G-C

Position:

• chr4-114717445-G-C

Variant summary

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

The XR_007058238.1(LOC124900763):​n.293+279C>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 0.035 in 151,896 control chromosomes in the GnomAD database, including 517 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 0.035 (517 hom., cov: 32)
• Consequence: LOC124900763 XR_007058238.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

LOC124900763 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900763	XR_007058238.1	n.293+279C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5329 AN: 151774 Hom.: 520 Cov.: 32

Gnomad AFR AF: 0.00550

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00767

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0350 AC: 5317 AN: 151896 Hom.: 517 Cov.: 32 AF XY: 0.0434 AC XY: 3220 AN XY: 74218

Gnomad4 AFR AF: 0.00548

Gnomad4 AMR AF: 0.0671

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0610

Gnomad4 NFE AF: 0.00767

Gnomad4 OTH AF: 0.0242

Alfa AF: 0.00367 Hom.: 0

Bravo AF: 0.0318

Asia WGS AF: 0.227 AC: 786 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78557978; hg19: chr4-115638601;