chr2-207234773-C-T

Position:

• chr2-207234773-C-T

Variant summary

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

The ENST00000448786.1(ENSG00000234902):​n.467+665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,036 control chromosomes in the GnomAD database, including 6,832 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 0.30 (6832 hom., cov: 32)
• Consequence: ENSG00000234902 ENST00000448786.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

ENSG00000234902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYOSLID-AS1	NR_110283.1	n.302+3047G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234902	ENST00000448786.1	n.467+665G>A		intron_variant		1
ENSG00000234902	ENST00000417096.5	n.284+665G>A		intron_variant		4
MYOSLID	ENST00000666421.1	n.79-10516C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45403 AN: 151918 Hom.: 6832 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.299 AC: 45429 AN: 152036 Hom.: 6832 Cov.: 32 AF XY: 0.296 AC XY: 22000 AN XY: 74312

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.305

Alfa AF: 0.246 Hom.: 1103

Bravo AF: 0.295

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs991684; hg19: chr2-208099497;