1-11728507-A-G

Variant names:

• chr1-11728507-A-G
• rs4846033
• ENST00000779472.1:n.178-1963T>C

Variant summary

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

The ENST00000779472.1(ENSG00000301523):​n.178-1963T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,268 control chromosomes in the GnomAD database, including 69,224 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 0.95 (69224 hom., cov: 33)
• Consequence: ENSG00000301523 ENST00000779472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710
• Publications: 14 publications found

Genes affected

ENSG00000301523 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779472.1. 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
	ENSG00000301523	ENST00000779472.1		n.178-1963T>C		intron	N/A
	ENSG00000301523	ENST00000779473.1		n.107-1963T>C		intron	N/A
	ENSG00000301523	ENST00000779474.1		n.165-1963T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144856 AN: 152150 Hom.: 69189 Cov.: 33

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.952 AC: 144945 AN: 152268 Hom.: 69224 Cov.: 33 AF XY: 0.953 AC XY: 70987 AN XY: 74466

African (AFR) AF: 0.871 AC: 36127 AN: 41498

American (AMR) AF: 0.973 AC: 14889 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3253 AN: 3472

East Asian (EAS) AF: 0.972 AC: 5043 AN: 5190

South Asian (SAS) AF: 0.984 AC: 4750 AN: 4826

European-Finnish (FIN) AF: 0.997 AC: 10595 AN: 10626

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67242 AN: 68036

Other (OTH) AF: 0.956 AC: 2020 AN: 2114

Alfa AF: 0.973 Hom.: 150661

Bravo AF: 0.945

Asia WGS AF: 0.973 AC: 3384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.82
PhyloP100		0.71

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: rs4846033;

hg19: chr1-11788564;