chr2-4451820-G-C

Variant names:

• chr2-4451820-G-C
• rs10495499
• ENST00000707165.1:n.506+789G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000707165.1(ENSG00000291325):​n.506+789G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 152,154 control chromosomes in the GnomAD database, including 86 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 0.027 (86 hom., cov: 32)
• Consequence: ENSG00000291325 ENST00000707165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 0 publications found

Genes affected

ENSG00000291325 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.027 (4108/152154) while in subpopulation NFE AF = 0.0439 (2984/67984). AF 95% confidence interval is 0.0426. There are 86 homozygotes in GnomAd4. There are 1920 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 86 gene

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
ENSG00000291325	ENST00000707165.1	n.506+789G>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4107 AN: 152036 Hom.: 86 Cov.: 32

Gnomad AFR AF: 0.00691

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0270 AC: 4108 AN: 152154 Hom.: 86 Cov.: 32 AF XY: 0.0258 AC XY: 1920 AN XY: 74396

African (AFR) AF: 0.00689 AC: 286 AN: 41512

American (AMR) AF: 0.0183 AC: 279 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5162

South Asian (SAS) AF: 0.0114 AC: 55 AN: 4828

European-Finnish (FIN) AF: 0.0333 AC: 353 AN: 10600

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0439 AC: 2984 AN: 67984

Other (OTH) AF: 0.0251 AC: 53 AN: 2112

Alfa AF: 0.0427 Hom.: 20

Bravo AF: 0.0237

Asia WGS AF: 0.0100 AC: 36 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.51
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs10495499; hg19: chr2-4499410;