1-209248964-G-C

Variant names:

• chr1-209248964-G-C
• rs2788153
• ENST00000654974.1:n.1457+11263C>G

Variant summary

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

The ENST00000654974.1(ENSG00000232537):​n.1457+11263C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 151,856 control chromosomes in the GnomAD database, including 55,421 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 0.84 (55421 hom., cov: 30)
• Consequence: ENSG00000232537 ENST00000654974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 2 publications found

Genes affected

ENSG00000232537 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372896	XR_922529.4	n.1458+11263C>G		intron_variant	Intron 2 of 3
LOC105372896	XR_922530.4	n.1458+11263C>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232537	ENST00000654974.1	n.1457+11263C>G		intron_variant	Intron 2 of 2
ENSG00000232537	ENST00000660754.1	n.74+11263C>G		intron_variant	Intron 1 of 2
ENSG00000232537	ENST00000666483.1	n.53+11263C>G		intron_variant	Intron 1 of 3
ENSG00000232537	ENST00000667236.1	n.53+11263C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.843 AC: 127893 AN: 151738 Hom.: 55403 Cov.: 30

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.843 AC: 127958 AN: 151856 Hom.: 55421 Cov.: 30 AF XY: 0.846 AC XY: 62743 AN XY: 74202

African (AFR) AF: 0.614 AC: 25373 AN: 41292

American (AMR) AF: 0.915 AC: 13966 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3151 AN: 3472

East Asian (EAS) AF: 0.974 AC: 4995 AN: 5128

South Asian (SAS) AF: 0.914 AC: 4395 AN: 4806

European-Finnish (FIN) AF: 0.938 AC: 9893 AN: 10550

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63176 AN: 68020

Other (OTH) AF: 0.866 AC: 1830 AN: 2114

Alfa AF: 0.878 Hom.: 7410

Bravo AF: 0.831

Asia WGS AF: 0.886 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.55
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2788153; hg19: chr1-209422309;