rs1856748

Variant names:

• chr1-206894495-T-C
• rs1856748
• ENST00000830172.1:n.177+1134A>G

Variant summary

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

The ENST00000830172.1(ENSG00000307982):​n.177+1134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 150,382 control chromosomes in the GnomAD database, including 16,821 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 0.47 (16821 hom., cov: 31)
• Consequence: ENSG00000307982 ENST00000830172.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 3 publications found

Genes affected

ENSG00000307982 (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 (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372879	XR_007066835.1	n.125+1499A>G		intron_variant	Intron 1 of 1
LOC105372879	XR_007066836.1	n.125+1499A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307982	ENST00000830172.1	n.177+1134A>G		intron_variant	Intron 1 of 1
ENSG00000307982	ENST00000830173.1	n.68+1134A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.468 AC: 70344 AN: 150266 Hom.: 16805 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.468 AC: 70415 AN: 150382 Hom.: 16821 Cov.: 31 AF XY: 0.459 AC XY: 33768 AN XY: 73536

African (AFR) AF: 0.577 AC: 23172 AN: 40184

American (AMR) AF: 0.463 AC: 7030 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1624 AN: 3454

East Asian (EAS) AF: 0.220 AC: 1132 AN: 5156

South Asian (SAS) AF: 0.233 AC: 1119 AN: 4800

European-Finnish (FIN) AF: 0.374 AC: 3948 AN: 10546

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.455 AC: 30816 AN: 67750

Other (OTH) AF: 0.494 AC: 1038 AN: 2102

Alfa AF: 0.463 Hom.: 3984

Bravo AF: 0.477

Asia WGS AF: 0.273 AC: 948 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	1.5
DANN	Benign	0.55
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs1856748; hg19: chr1-207067840;