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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830172.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307982	ENST00000830172.1		n.177+1134A>G		intron	N/A
	ENSG00000307982	ENST00000830173.1		n.68+1134A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1856748;

hg19: chr1-207067840;