1-180969922-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000243155 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243155	ENST00000358073.2	n.365+6196G>C		intron_variant	Intron 1 of 1	2

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

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.716

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7549545; hg19: chr1-180939058;