chr2-210180758-T-C

Variant names:

• chr2-210180758-T-C
• rs1396828
• ENST00000412065.1:n.312+8929T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412065.1(ENSG00000279317):​n.312+8929T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,014 control chromosomes in the GnomAD database, including 13,210 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 0.39 (13210 hom., cov: 32)
• Consequence: ENSG00000279317 ENST00000412065.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

Genes affected

ENSG00000279317 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 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	ENST00000412065.1	n.312+8929T>C		intron_variant	Intron 1 of 2	4
ENSG00000279317	ENST00000639259.2	n.279+8929T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59031 AN: 151896 Hom.: 13195 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.389 AC: 59064 AN: 152014 Hom.: 13210 Cov.: 32 AF XY: 0.395 AC XY: 29350 AN XY: 74284

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.426

Alfa AF: 0.453 Hom.: 28064

Bravo AF: 0.380

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1396828; hg19: chr2-211045482;