chr1-116495665-T-C

Variant names:

• chr1-116495665-T-C
• rs12025416
• ENST00000456414.2:n.412-759A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456414.2(ENSG00000224950):​n.412-759A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,220 control chromosomes in the GnomAD database, including 13,494 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 0.34 (13494 hom., cov: 33)
• Consequence: ENSG00000224950 ENST00000456414.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943

Genes affected

ENSG00000224950 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268235	XR_002958352.2	n.14272+2172T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224950	ENST00000456414.2	n.412-759A>G		intron_variant	Intron 1 of 1	2
ENSG00000286276	ENST00000660250.1	n.144+2172T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51446 AN: 152102 Hom.: 13445 Cov.: 33

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.339 AC: 51552 AN: 152220 Hom.: 13494 Cov.: 33 AF XY: 0.346 AC XY: 25768 AN XY: 74438

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.290

Alfa AF: 0.0921 Hom.: 152

Bravo AF: 0.359

Asia WGS AF: 0.503 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12025416; hg19: chr1-117038287;