2-47947060-T-C

Position:

• chr2-47947060-T-C

Variant summary

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

The ENST00000651429.1(ENSG00000230773):​n.807+1907A>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 0.717 in 152,086 control chromosomes in the GnomAD database, including 40,337 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 0.72 (40337 hom., cov: 32)
• Consequence: ENST00000651429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374591	XR_001739454.2	n.456-3448A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000447571.5	n.467+1324A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000651429.1	n.807+1907A>G		intron_variant, non_coding_transcript_variant
	ENST00000587616.1	n.1322-1773A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000649883.1	n.428+1324A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108954 AN: 151974 Hom.: 40289 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.717 AC: 109056 AN: 152086 Hom.: 40337 Cov.: 32 AF XY: 0.717 AC XY: 53308 AN XY: 74316

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.702

Alfa AF: 0.646 Hom.: 50339

Bravo AF: 0.737

Asia WGS AF: 0.822 AC: 2861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	14
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6729916; hg19: chr2-48174199;