4-129367465-A-G

Position:

• chr4-129367465-A-G

Variant summary

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

The ENST00000659495.1(ENSG00000287748):​n.112-4280T>C 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 0.0914 in 152,250 control chromosomes in the GnomAD database, including 864 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 0.091 (864 hom., cov: 33)
• Consequence: ENST00000659495.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377417	XR_939191.3	n.365-4280T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659495.1	n.112-4280T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0914 AC: 13899 AN: 152132 Hom.: 862 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0914 AC: 13921 AN: 152250 Hom.: 864 Cov.: 33 AF XY: 0.0929 AC XY: 6914 AN XY: 74438

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0595

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.0512

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0618 Hom.: 152

Bravo AF: 0.105

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11942914; hg19: chr4-130288620;