chr1-118481017-C-T

Variant names:

• chr1-118481017-C-T
• rs1229119
• ENST00000746228.1:n.579+14168G>A

Variant summary

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

The ENST00000746228.1(ENSG00000297215):​n.579+14168G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,898 control chromosomes in the GnomAD database, including 11,100 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 0.38 (11100 hom., cov: 32)
• Consequence: ENSG00000297215 ENST00000746228.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 5 publications found

Genes affected

ENSG00000297215 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746228.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297215	ENST00000746228.1		n.579+14168G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57512 AN: 151780 Hom.: 11084 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.379 AC: 57560 AN: 151898 Hom.: 11100 Cov.: 32 AF XY: 0.382 AC XY: 28336 AN XY: 74204

African (AFR) AF: 0.316 AC: 13074 AN: 41406

American (AMR) AF: 0.408 AC: 6232 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2574 AN: 5170

South Asian (SAS) AF: 0.451 AC: 2177 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4653 AN: 10532

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26495 AN: 67932

Other (OTH) AF: 0.385 AC: 811 AN: 2106

Alfa AF: 0.387 Hom.: 19390

Bravo AF: 0.376

Asia WGS AF: 0.453 AC: 1575 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.081
DANN	Benign	0.70
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1229119; hg19: chr1-119023640;