4-127420965-T-C

Position:

• chr4-127420965-T-C

Variant summary

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

The ENST00000504050.5(ENSG00000248491):​n.119-5803A>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 0.54 in 151,824 control chromosomes in the GnomAD database, including 23,267 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 0.54 (23267 hom., cov: 31)
• Consequence: ENST00000504050.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724210	XR_001741824.3	n.122-5803A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000504050.5	n.119-5803A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000509671.1	n.207-19205A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000661442.1	n.114-5803A>G		intron_variant, non_coding_transcript_variant
	ENST00000667124.1	n.115-5803A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81968 AN: 151706 Hom.: 23230 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.540 AC: 82057 AN: 151824 Hom.: 23267 Cov.: 31 AF XY: 0.531 AC XY: 39415 AN XY: 74182

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.564

Alfa AF: 0.506 Hom.: 40848

Bravo AF: 0.569

Asia WGS AF: 0.415 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
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: rs724950; hg19: chr4-128342120;