rs10079205

Variant names:

• chr5-4197861-C-G
• rs10079205
• ENST00000762810.1:n.547-208C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-4197861-C-G
• chr5-4197861-C-T

Variant summary

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

The ENST00000762810.1(ENSG00000299354):​n.547-208C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,154 control chromosomes in the GnomAD database, including 57,480 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 0.86 (57480 hom., cov: 33)
• Consequence: ENSG00000299354 ENST00000762810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 3 publications found

Genes affected

ENSG00000299354 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762810.1. 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
	ENSG00000299354	ENST00000762810.1		n.547-208C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130124 AN: 152038 Hom.: 57482 Cov.: 33

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.855 AC: 130148 AN: 152154 Hom.: 57480 Cov.: 33 AF XY: 0.858 AC XY: 63829 AN XY: 74388

African (AFR) AF: 0.609 AC: 25244 AN: 41448

American (AMR) AF: 0.923 AC: 14110 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3203 AN: 3470

East Asian (EAS) AF: 0.968 AC: 4994 AN: 5160

South Asian (SAS) AF: 0.899 AC: 4331 AN: 4820

European-Finnish (FIN) AF: 0.985 AC: 10457 AN: 10620

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64858 AN: 68024

Other (OTH) AF: 0.856 AC: 1808 AN: 2112

Alfa AF: 0.886 Hom.: 3604

Bravo AF: 0.841

Asia WGS AF: 0.879 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.33
PhyloP100		-1.8

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: rs10079205;

hg19: chr5-4197974;