4-180038634-T-C

Variant names:

• chr4-180038634-T-C
• rs1112857
• ENST00000663768.1:n.504-17243A>G

Variant summary

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

The ENST00000663768.1(ENSG00000287083):​n.504-17243A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,126 control chromosomes in the GnomAD database, including 7,026 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 0.28 (7026 hom., cov: 33)
• Consequence: ENSG00000287083 ENST00000663768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 6 publications found

Genes affected

ENSG00000287083 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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
ENSG00000287083	ENST00000663768.1	n.504-17243A>G		intron_variant	Intron 2 of 6
ENSG00000287083	ENST00000826563.1	n.147-17243A>G		intron_variant	Intron 1 of 6
ENSG00000287083	ENST00000826564.1	n.256-17243A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42387 AN: 152008 Hom.: 7024 Cov.: 33

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.279 AC: 42384 AN: 152126 Hom.: 7026 Cov.: 33 AF XY: 0.280 AC XY: 20805 AN XY: 74356

African (AFR) AF: 0.0917 AC: 3812 AN: 41552

American (AMR) AF: 0.266 AC: 4063 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1967 AN: 5160

South Asian (SAS) AF: 0.331 AC: 1598 AN: 4824

European-Finnish (FIN) AF: 0.409 AC: 4320 AN: 10566

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24553 AN: 67968

Other (OTH) AF: 0.265 AC: 560 AN: 2114

Alfa AF: 0.329 Hom.: 25035

Bravo AF: 0.260

Asia WGS AF: 0.311 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.87
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1112857; hg19: chr4-180959787;