chr4-105143469-T-TA

Variant names:

• chr4-105143469-T-TA
• rs34480284
• XM_047416559.1:c.*778+2025dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000776606.1(ENSG00000251259):​n.148+4201_148+4202insT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (20534 hom., cov: 0)
• Consequence: ENSG00000251259 ENST00000776606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 6 publications found

Genes affected

LOC124900868 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776606.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251259	ENST00000776606.1		n.148+4201_148+4202insT		intron	N/A
	ENSG00000251259	ENST00000776607.1		n.370+958_370+959insT		intron	N/A
	ENSG00000251259	ENST00000776608.1		n.242-2878_242-2877insT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77095 AN: 151466 Hom.: 20496 Cov.: 0

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.509 AC: 77194 AN: 151584 Hom.: 20534 Cov.: 0 AF XY: 0.521 AC XY: 38576 AN XY: 74040

African (AFR) AF: 0.620 AC: 25638 AN: 41340

American (AMR) AF: 0.526 AC: 8016 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1764 AN: 3466

East Asian (EAS) AF: 0.812 AC: 4200 AN: 5172

South Asian (SAS) AF: 0.588 AC: 2816 AN: 4790

European-Finnish (FIN) AF: 0.531 AC: 5534 AN: 10430

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27653 AN: 67842

Other (OTH) AF: 0.513 AC: 1082 AN: 2108

Alfa AF: 0.261 Hom.: 438

Asia WGS AF: 0.689 AC: 2389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.046

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs34480284;

hg19: chr4-106064626;