1-159709846-A-C

Variant names:

• chr1-159709846-A-C
• rs3093077
• ENST00000751816.1:n.108-16681A>C

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-16681A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,230 control chromosomes in the GnomAD database, including 2,276 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 0.14 (2276 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 89 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913	ENST00000751816.1		n.108-16681A>C		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-16681A>C		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-16681A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20644 AN: 152112 Hom.: 2265 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.136 AC: 20686 AN: 152230 Hom.: 2276 Cov.: 32 AF XY: 0.135 AC XY: 10015 AN XY: 74438

African (AFR) AF: 0.301 AC: 12499 AN: 41496

American (AMR) AF: 0.0769 AC: 1177 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3470

East Asian (EAS) AF: 0.155 AC: 802 AN: 5182

South Asian (SAS) AF: 0.113 AC: 548 AN: 4830

European-Finnish (FIN) AF: 0.0663 AC: 704 AN: 10622

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4175 AN: 68008

Other (OTH) AF: 0.133 AC: 282 AN: 2116

Alfa AF: 0.0834 Hom.: 2992

Bravo AF: 0.143

Asia WGS AF: 0.113 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.66
PhyloP100		-0.79

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: rs3093077;

hg19: chr1-159679636;