rs7578859

Variant names:

• chr2-208130203-C-A
• rs7578859
• ENST00000728538.1:n.101-6853C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-208130203-C-A
• chr2-208130203-C-G

Variant summary

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

The ENST00000728538.1(ENSG00000295187):​n.101-6853C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,038 control chromosomes in the GnomAD database, including 34,914 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 0.67 (34914 hom., cov: 32)
• Consequence: ENSG00000295187 ENST00000728538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 1 publications found

Genes affected

ENSG00000295187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507443	NR_038437.1	n.98-6853C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295187	ENST00000728538.1	n.101-6853C>A		intron_variant	Intron 1 of 2
ENSG00000295187	ENST00000728539.1	n.118-6853C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102072 AN: 151920 Hom.: 34869 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.672 AC: 102174 AN: 152038 Hom.: 34914 Cov.: 32 AF XY: 0.666 AC XY: 49473 AN XY: 74326

African (AFR) AF: 0.655 AC: 27144 AN: 41450

American (AMR) AF: 0.569 AC: 8693 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2272 AN: 3472

East Asian (EAS) AF: 0.420 AC: 2174 AN: 5172

South Asian (SAS) AF: 0.583 AC: 2815 AN: 4826

European-Finnish (FIN) AF: 0.712 AC: 7516 AN: 10552

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49277 AN: 67972

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

Alfa AF: 0.635 Hom.: 4188

Bravo AF: 0.661

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.9
DANN	Benign	0.71
PhyloP100		-0.010
PromoterAI		0.056	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7578859; hg19: chr2-208994927;