chr1-89773992-A-G

Variant names:

• chr1-89773992-A-G
• rs1215582
• ENST00000370453.5:n.139-69646A>G

Variant summary

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

The ENST00000370453.5(ENSG00000271949):​n.139-69646A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.984 in 152,312 control chromosomes in the GnomAD database, including 73,777 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 0.98 (73777 hom., cov: 31)
• Consequence: ENSG00000271949 ENST00000370453.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 1 publications found

Genes affected

ENSG00000271949 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985744	XR_001738140.2	n.898+1174A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271949	ENST00000370453.5	n.139-69646A>G		intron_variant	Intron 2 of 3	5		ENSP00000359482.5

Frequencies

GnomAD3 genomes AF: 0.984 AC: 149761 AN: 152194 Hom.: 73717 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.989

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

GnomAD4 genome AF: 0.984 AC: 149880 AN: 152312 Hom.: 73777 Cov.: 31 AF XY: 0.985 AC XY: 73314 AN XY: 74464

African (AFR) AF: 0.946 AC: 39277 AN: 41538

American (AMR) AF: 0.991 AC: 15177 AN: 15308

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5186

South Asian (SAS) AF: 1.00 AC: 4825 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10620 AN: 10620

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68028 AN: 68042

Other (OTH) AF: 0.989 AC: 2090 AN: 2114

Alfa AF: 0.995 Hom.: 87549

Bravo AF: 0.982

Asia WGS AF: 0.998 AC: 3472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.35
PhyloP100		-0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1215582; hg19: chr1-90239551;