rs127557

Variant names:

• chr1-228792151-G-A
• rs127557
• ENST00000840982.1:n.145+9082G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-228792151-G-A
• chr1-228792151-G-C

Variant summary

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

The ENST00000840982.1(ENSG00000309426):​n.145+9082G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,980 control chromosomes in the GnomAD database, including 22,048 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 0.52 (22048 hom., cov: 32)
• Consequence: ENSG00000309426 ENST00000840982.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 2 publications found

Genes affected

ENSG00000309426 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840982.1. 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
	ENSG00000309426	ENST00000840982.1		n.145+9082G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78419 AN: 151862 Hom.: 22037 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.516 AC: 78468 AN: 151980 Hom.: 22048 Cov.: 32 AF XY: 0.521 AC XY: 38689 AN XY: 74276

African (AFR) AF: 0.274 AC: 11350 AN: 41436

American (AMR) AF: 0.591 AC: 9031 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1902 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2475 AN: 5138

South Asian (SAS) AF: 0.543 AC: 2618 AN: 4818

European-Finnish (FIN) AF: 0.700 AC: 7395 AN: 10562

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42091 AN: 67970

Other (OTH) AF: 0.543 AC: 1147 AN: 2112

Alfa AF: 0.580 Hom.: 35139

Bravo AF: 0.494

Asia WGS AF: 0.509 AC: 1772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.83
DANN	Benign	0.64
PhyloP100		-0.093

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: rs127557;

hg19: chr1-228927898;