4-116954105-T-G

Variant names:

• chr4-116954105-T-G
• rs1440306
• ENST00000824997.1:n.213-1243A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000824997.1(ENSG00000287290):​n.213-1243A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,898 control chromosomes in the GnomAD database, including 3,870 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 0.22 (3870 hom., cov: 32)
• Consequence: ENSG00000287290 ENST00000824997.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 6 publications found

Genes affected

ENSG00000287290 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824997.1. 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
	ENSG00000287290	ENST00000824997.1		n.213-1243A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33843 AN: 151778 Hom.: 3868 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.223 AC: 33861 AN: 151898 Hom.: 3870 Cov.: 32 AF XY: 0.223 AC XY: 16525 AN XY: 74238

African (AFR) AF: 0.208 AC: 8635 AN: 41488

American (AMR) AF: 0.250 AC: 3810 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3464

East Asian (EAS) AF: 0.281 AC: 1436 AN: 5110

South Asian (SAS) AF: 0.270 AC: 1302 AN: 4822

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10606

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15034 AN: 67856

Other (OTH) AF: 0.261 AC: 550 AN: 2106

Alfa AF: 0.208 Hom.: 2060

Bravo AF: 0.226

Asia WGS AF: 0.270 AC: 939 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs1440306; hg19: chr4-117875261;