2-210318773-C-T

Variant names:

• chr2-210318773-C-T
• rs925274
• ENST00000795993.1:n.388+38912C>T

Variant summary

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

The ENST00000795993.1(ENSG00000279317):​n.388+38912C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,680 control chromosomes in the GnomAD database, including 9,741 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 0.36 (9741 hom., cov: 31)
• Consequence: ENSG00000279317 ENST00000795993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 3 publications found

Genes affected

ENSG00000279317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 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
ENSG00000279317	ENST00000795993.1	n.388+38912C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53835 AN: 151562 Hom.: 9726 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.355 AC: 53907 AN: 151680 Hom.: 9741 Cov.: 31 AF XY: 0.362 AC XY: 26804 AN XY: 74112

African (AFR) AF: 0.364 AC: 15054 AN: 41364

American (AMR) AF: 0.453 AC: 6897 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1414 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2319 AN: 5114

South Asian (SAS) AF: 0.347 AC: 1660 AN: 4786

European-Finnish (FIN) AF: 0.367 AC: 3852 AN: 10488

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21411 AN: 67918

Other (OTH) AF: 0.378 AC: 794 AN: 2100

Alfa AF: 0.346 Hom.: 1843

Bravo AF: 0.362

Asia WGS AF: 0.447 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.43
DANN	Benign	0.49
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs925274; hg19: chr2-211183497;