1-25916391-G-A

Variant names:

• chr1-25916391-G-A
• rs807061
• ENST00000722475.1:n.257+201C>T

Variant summary

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

The ENST00000722475.1(ENSG00000294284):​n.257+201C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,006 control chromosomes in the GnomAD database, including 33,093 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 0.63 (33093 hom., cov: 32)
• Consequence: ENSG00000294284 ENST00000722475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 5 publications found

Genes affected

ENSG00000294284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722475.1. 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
	ENSG00000294284	ENST00000722475.1		n.257+201C>T		intron	N/A
	ENSG00000294284	ENST00000722476.1		n.113+201C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96442 AN: 151888 Hom.: 33075 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.635 AC: 96489 AN: 152006 Hom.: 33093 Cov.: 32 AF XY: 0.639 AC XY: 47463 AN XY: 74276

African (AFR) AF: 0.350 AC: 14497 AN: 41410

American (AMR) AF: 0.733 AC: 11196 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2303 AN: 3472

East Asian (EAS) AF: 0.693 AC: 3583 AN: 5168

South Asian (SAS) AF: 0.843 AC: 4055 AN: 4812

European-Finnish (FIN) AF: 0.722 AC: 7639 AN: 10576

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50965 AN: 67970

Other (OTH) AF: 0.646 AC: 1364 AN: 2112

Alfa AF: 0.708 Hom.: 151991

Bravo AF: 0.613

Asia WGS AF: 0.767 AC: 2668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs807061; hg19: chr1-26242882;