chr1-159672559-G-C

Variant names:

• chr1-159672559-G-C
• rs1811472
• ENST00000751816.1:n.107+11870G>C

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.107+11870G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,066 control chromosomes in the GnomAD database, including 12,606 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 0.40 (12606 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 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.107+11870G>C		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.109+11870G>C		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.62+11870G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60092 AN: 151948 Hom.: 12602 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.395 AC: 60119 AN: 152066 Hom.: 12606 Cov.: 32 AF XY: 0.398 AC XY: 29591 AN XY: 74364

African (AFR) AF: 0.310 AC: 12854 AN: 41468

American (AMR) AF: 0.468 AC: 7151 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4054 AN: 5180

South Asian (SAS) AF: 0.338 AC: 1633 AN: 4832

European-Finnish (FIN) AF: 0.410 AC: 4330 AN: 10558

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27165 AN: 67948

Other (OTH) AF: 0.399 AC: 843 AN: 2114

Alfa AF: 0.389 Hom.: 1649

Bravo AF: 0.399

Asia WGS AF: 0.569 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.091
DANN	Benign	0.52
PhyloP100		-0.32

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: rs1811472;

hg19: chr1-159642349;