rs2204779

Variant names:

• chr7-118798130-T-C
• rs2204779
• ENST00000761310.1:n.151-33557A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-118798130-T-C
• chr7-118798130-T-G

Variant summary

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

The ENST00000761310.1(ENSG00000299159):​n.151-33557A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 152,242 control chromosomes in the GnomAD database, including 1,802 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 0.090 (1802 hom., cov: 33)
• Consequence: ENSG00000299159 ENST00000761310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 2 publications found

Genes affected

ENSG00000299159 (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 (AFR) allele frequency at 95% confidence interval = 0.286 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
ENSG00000299159	ENST00000761310.1	n.151-33557A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13608 AN: 152124 Hom.: 1793 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00958

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0897 AC: 13649 AN: 152242 Hom.: 1802 Cov.: 33 AF XY: 0.0868 AC XY: 6462 AN XY: 74460

African (AFR) AF: 0.290 AC: 12033 AN: 41482

American (AMR) AF: 0.0370 AC: 566 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4828

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10620

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00958 AC: 652 AN: 68032

Other (OTH) AF: 0.0695 AC: 147 AN: 2116

Alfa AF: 0.0228 Hom.: 130

Bravo AF: 0.100

Asia WGS AF: 0.0200 AC: 68 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs2204779; hg19: chr7-118438184;