chr2-212967998-T-C

Position:

• chr2-212967998-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000415387.1(ENSG00000273118):​n.81+53467A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,066 control chromosomes in the GnomAD database, including 7,011 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 0.29 (7011 hom., cov: 32)
• Consequence: ENST00000415387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102725082	XR_007088066.1	n.17279-2483A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000415387.1	n.81+53467A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43720 AN: 151948 Hom.: 7007 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.288 AC: 43743 AN: 152066 Hom.: 7011 Cov.: 32 AF XY: 0.292 AC XY: 21720 AN XY: 74344

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.306

Alfa AF: 0.290 Hom.: 1451

Bravo AF: 0.302

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	18
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6740906; hg19: chr2-213832722;