1-180969922-C-G

Variant names:

• chr1-180969922-C-G
• rs7549545
• ENST00000358073.2:n.365+6196G>C

Variant summary

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

The ENST00000358073.2(ENSG00000243155):​n.365+6196G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,048 control chromosomes in the GnomAD database, including 38,571 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 0.71 (38571 hom., cov: 31)
• Consequence: ENSG00000243155 ENST00000358073.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 3 publications found

Genes affected

ENSG00000243155 (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 (SAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000358073.2. 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
	ENSG00000243155	ENST00000358073.2	TSL:2	n.365+6196G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107994 AN: 151930 Hom.: 38551 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.711 AC: 108060 AN: 152048 Hom.: 38571 Cov.: 31 AF XY: 0.712 AC XY: 52925 AN XY: 74316

African (AFR) AF: 0.663 AC: 27486 AN: 41452

American (AMR) AF: 0.719 AC: 10991 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2405 AN: 3472

East Asian (EAS) AF: 0.607 AC: 3135 AN: 5162

South Asian (SAS) AF: 0.778 AC: 3740 AN: 4810

European-Finnish (FIN) AF: 0.736 AC: 7786 AN: 10574

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.735 AC: 49974 AN: 67976

Other (OTH) AF: 0.716 AC: 1509 AN: 2108

Alfa AF: 0.713 Hom.: 4809

Bravo AF: 0.707

Asia WGS AF: 0.739 AC: 2572 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	2.4
DANN	Benign	0.74
PhyloP100		0.12

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: rs7549545;

hg19: chr1-180939058;