chr4-127420965-T-C

Variant names:

• chr4-127420965-T-C
• rs724950
• ENST00000504050.6:n.149-5803A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661442.1(ENSG00000248491):​n.114-5803A>G variant causes a intron 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: ENSG00000248491 ENST00000661442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

Genes affected

ENSG00000248491 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661442.1. 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
	ENSG00000248491	ENST00000504050.6	TSL:5	n.149-5803A>G		intron	N/A
	ENSG00000248491	ENST00000509671.1	TSL:5	n.207-19205A>G		intron	N/A
	ENSG00000248491	ENST00000661442.1		n.114-5803A>G		intron	N/A

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

African (AFR) AF: 0.678 AC: 28074 AN: 41392

American (AMR) AF: 0.628 AC: 9551 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1828 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1902 AN: 5142

South Asian (SAS) AF: 0.389 AC: 1875 AN: 4820

European-Finnish (FIN) AF: 0.336 AC: 3541 AN: 10552

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33458 AN: 67910

Other (OTH) AF: 0.564 AC: 1192 AN: 2112

Alfa AF: 0.514 Hom.: 90067

Bravo AF: 0.569

Asia WGS AF: 0.415 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.65
PhyloP100		0.34

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: rs724950;

hg19: chr4-128342120;