rs7525160

Variant names:

• chr1-207495069-G-C
• rs7525160
• ENST00000809561.1:n.*81C>G

Variant summary

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

The ENST00000809561.1(ENSG00000305204):​n.*81C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,666 control chromosomes in the GnomAD database, including 7,555 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 0.30 (7555 hom., cov: 31)
• Consequence: ENSG00000305204 ENST00000809561.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 13 publications found

Genes affected

ENSG00000305204 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809561.1. 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
	ENSG00000305204	ENST00000809561.1		n.*81C>G		downstream_gene	N/A
	ENSG00000305204	ENST00000809562.1		n.*74C>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45472 AN: 151550 Hom.: 7547 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.300 AC: 45485 AN: 151666 Hom.: 7555 Cov.: 31 AF XY: 0.310 AC XY: 22938 AN XY: 74106

African (AFR) AF: 0.165 AC: 6826 AN: 41314

American (AMR) AF: 0.444 AC: 6775 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3468

East Asian (EAS) AF: 0.442 AC: 2273 AN: 5144

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4812

European-Finnish (FIN) AF: 0.373 AC: 3899 AN: 10444

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21343 AN: 67914

Other (OTH) AF: 0.287 AC: 607 AN: 2112

Alfa AF: 0.312 Hom.: 957

Bravo AF: 0.300

Asia WGS AF: 0.456 AC: 1585 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.31
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7525160; hg19: chr1-207668414;