1-157440899-C-G

Variant names:

• chr1-157440899-C-G
• rs2309879
• ENST00000777025.1:n.167+1146G>C

Variant summary

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

The ENST00000777025.1(ENSG00000301209):​n.167+1146G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,094 control chromosomes in the GnomAD database, including 6,722 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 (6722 hom., cov: 32)
• Consequence: ENSG00000301209 ENST00000777025.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 1 publications found

Genes affected

ENSG00000301209 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000777025.1. 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
	ENSG00000301209	ENST00000777025.1		n.167+1146G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43216 AN: 151974 Hom.: 6725 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0637

Gnomad SAS AF: 0.0975

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.284 AC: 43230 AN: 152094 Hom.: 6722 Cov.: 32 AF XY: 0.281 AC XY: 20856 AN XY: 74342

African (AFR) AF: 0.201 AC: 8333 AN: 41498

American (AMR) AF: 0.373 AC: 5701 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3472

East Asian (EAS) AF: 0.0641 AC: 332 AN: 5182

South Asian (SAS) AF: 0.0976 AC: 470 AN: 4818

European-Finnish (FIN) AF: 0.272 AC: 2875 AN: 10570

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23172 AN: 67964

Other (OTH) AF: 0.305 AC: 643 AN: 2110

Alfa AF: 0.171 Hom.: 368

Bravo AF: 0.290

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.37
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2309879;

hg19: chr1-157410689;