chr1-165629409-C-G

Variant names:

• chr1-165629409-C-G
• rs7549530
• ENST00000820306.1:n.267-179G>C

Variant summary

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

The ENST00000820306.1(ENSG00000306707):​n.267-179G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,966 control chromosomes in the GnomAD database, including 2,049 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 0.16 (2049 hom., cov: 33)
• Consequence: ENSG00000306707 ENST00000820306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.811
• Publications: 3 publications found

Genes affected

ENSG00000306707 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820306.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306707	ENST00000820306.1		n.267-179G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24038 AN: 151848 Hom.: 2044 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.158 AC: 24057 AN: 151966 Hom.: 2049 Cov.: 33 AF XY: 0.154 AC XY: 11427 AN XY: 74276

African (AFR) AF: 0.200 AC: 8270 AN: 41386

American (AMR) AF: 0.173 AC: 2640 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3466

East Asian (EAS) AF: 0.0447 AC: 232 AN: 5186

South Asian (SAS) AF: 0.103 AC: 495 AN: 4820

European-Finnish (FIN) AF: 0.0994 AC: 1050 AN: 10568

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10630 AN: 67946

Other (OTH) AF: 0.156 AC: 330 AN: 2112

Alfa AF: 0.151 Hom.: 240

Bravo AF: 0.165

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.68
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs7549530; hg19: chr1-165598646;