4-129416904-T-C

Variant names:

• chr4-129416904-T-C
• rs1433375
• ENST00000723085.1:n.178-4180A>G

Variant summary

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

The ENST00000723085.1(ENSG00000287748):​n.178-4180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,054 control chromosomes in the GnomAD database, including 24,052 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 0.53 (24052 hom., cov: 32)
• Consequence: ENSG00000287748 ENST00000723085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 4 publications found

Genes affected

ENSG00000287748 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287748	ENST00000723085.1	n.178-4180A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80401 AN: 151936 Hom.: 24006 Cov.: 32

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.529 AC: 80508 AN: 152054 Hom.: 24052 Cov.: 32 AF XY: 0.530 AC XY: 39374 AN XY: 74322

African (AFR) AF: 0.816 AC: 33870 AN: 41520

American (AMR) AF: 0.390 AC: 5945 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3472

East Asian (EAS) AF: 0.633 AC: 3257 AN: 5144

South Asian (SAS) AF: 0.442 AC: 2128 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5024 AN: 10558

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27360 AN: 67976

Other (OTH) AF: 0.526 AC: 1110 AN: 2112

Alfa AF: 0.432 Hom.: 26685

Bravo AF: 0.536

Asia WGS AF: 0.580 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.65
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1433375; hg19: chr4-130338059;