2-47947060-T-C

Variant names:

• chr2-47947060-T-C
• rs6729916
• ENST00000447571.5:n.467+1324A>G

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.467+1324A>G variant causes a intron 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: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593
• Publications: 3 publications found

Genes affected

ENSG00000230773 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105374591	XR_001739454.2	n.456-3448A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230773	ENST00000447571.5	n.467+1324A>G		intron_variant	Intron 6 of 8	1
ENSG00000230773	ENST00000587616.1	n.1322-1773A>G		intron_variant	Intron 10 of 10	5
ENSG00000230773	ENST00000649883.1	n.428+1324A>G		intron_variant	Intron 6 of 8

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

African (AFR) AF: 0.888 AC: 36889 AN: 41528

American (AMR) AF: 0.708 AC: 10814 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2442 AN: 3470

East Asian (EAS) AF: 0.924 AC: 4797 AN: 5190

South Asian (SAS) AF: 0.702 AC: 3381 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6122 AN: 10516

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42357 AN: 67976

Other (OTH) AF: 0.702 AC: 1482 AN: 2110

Alfa AF: 0.660 Hom.: 125827

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
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs6729916; hg19: chr2-48174199;