4-127420965-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 ENST00000504050.6(ENSG00000248491):​n.149-5803A>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 ENST00000504050.6 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724210	XR_001741824.3	n.122-5803A>G		intron_variant	Intron 1 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248491	ENST00000504050.6	n.149-5803A>G		intron_variant	Intron 1 of 5	5
ENSG00000248491	ENST00000509671.1	n.207-19205A>G		intron_variant	Intron 2 of 2	5
ENSG00000248491	ENST00000661442.1	n.114-5803A>G		intron_variant	Intron 1 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs724950; hg19: chr4-128342120;