chr1-228195666-G-A

Variant names:

• chr1-228195666-G-A
• rs1557026
• ENST00000805142.1:n.102+899G>A

Variant summary

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

The ENST00000805142.1(ENSG00000304651):​n.102+899G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,000 control chromosomes in the GnomAD database, including 6,857 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 0.29 (6857 hom., cov: 32)
• Consequence: ENSG00000304651 ENST00000805142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 1 publications found

Genes affected

ENSG00000304651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904536	XR_007066917.1	n.7072+899G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304651	ENST00000805142.1	n.102+899G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44200 AN: 151882 Hom.: 6849 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.291 AC: 44233 AN: 152000 Hom.: 6857 Cov.: 32 AF XY: 0.285 AC XY: 21194 AN XY: 74266

African (AFR) AF: 0.205 AC: 8478 AN: 41450

American (AMR) AF: 0.303 AC: 4625 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3472

East Asian (EAS) AF: 0.170 AC: 877 AN: 5150

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4816

European-Finnish (FIN) AF: 0.279 AC: 2942 AN: 10552

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23952 AN: 67966

Other (OTH) AF: 0.307 AC: 647 AN: 2110

Alfa AF: 0.307 Hom.: 890

Bravo AF: 0.288

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.52
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1557026; hg19: chr1-228383367;