4-112472287-T-C

Variant names:

• chr4-112472287-T-C
• rs1486860
• ENST00000843046.1:n.34-23603A>G

Variant summary

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

The ENST00000843046.1(ENSG00000309690):​n.34-23603A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,006 control chromosomes in the GnomAD database, including 11,967 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 0.39 (11967 hom., cov: 32)
• Consequence: ENSG00000309690 ENST00000843046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 4 publications found

Genes affected

ENSG00000309690 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843046.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309690	ENST00000843046.1		n.34-23603A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59890 AN: 151888 Hom.: 11961 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.394 AC: 59926 AN: 152006 Hom.: 11967 Cov.: 32 AF XY: 0.395 AC XY: 29357 AN XY: 74286

African (AFR) AF: 0.396 AC: 16428 AN: 41460

American (AMR) AF: 0.478 AC: 7295 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1731 AN: 5176

South Asian (SAS) AF: 0.448 AC: 2157 AN: 4816

European-Finnish (FIN) AF: 0.378 AC: 3985 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26054 AN: 67960

Other (OTH) AF: 0.382 AC: 807 AN: 2110

Alfa AF: 0.389 Hom.: 19271

Bravo AF: 0.402

Asia WGS AF: 0.453 AC: 1572 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.8
DANN	Benign	0.43
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs1486860; hg19: chr4-113393443;