2-210745177-C-G

Variant names:

• chr2-210745177-C-G
• rs10490325
• ENST00000737540.1:n.435+9578C>G

Variant summary

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

The ENST00000737540.1(ENSG00000296241):​n.435+9578C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,106 control chromosomes in the GnomAD database, including 2,145 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 0.15 (2145 hom., cov: 32)
• Consequence: ENSG00000296241 ENST00000737540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 5 publications found

Genes affected

ENSG00000296241 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 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
ENSG00000296241	ENST00000737540.1	n.435+9578C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22702 AN: 151988 Hom.: 2141 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.149 AC: 22703 AN: 152106 Hom.: 2145 Cov.: 32 AF XY: 0.155 AC XY: 11553 AN XY: 74348

African (AFR) AF: 0.0348 AC: 1444 AN: 41518

American (AMR) AF: 0.200 AC: 3053 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3470

East Asian (EAS) AF: 0.153 AC: 792 AN: 5162

South Asian (SAS) AF: 0.188 AC: 910 AN: 4828

European-Finnish (FIN) AF: 0.287 AC: 3028 AN: 10550

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12404 AN: 67990

Other (OTH) AF: 0.143 AC: 303 AN: 2112

Alfa AF: 0.0737 Hom.: 132

Bravo AF: 0.138

Asia WGS AF: 0.161 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.66
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10490325; hg19: chr2-211609901;