chr2-48024017-G-T

Variant names:

• chr2-48024017-G-T
• rs11681243
• ENST00000447571.5:n.241-20592C>A

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.241-20592C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,116 control chromosomes in the GnomAD database, including 905 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 0.10 (905 hom., cov: 32)
• Consequence: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447571.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230773	ENST00000447571.5	TSL:1	n.241-20592C>A		intron	N/A
	ENSG00000230773	ENST00000587616.1	TSL:5	n.191-1614C>A		intron	N/A
	ENSG00000230773	ENST00000649883.1		n.202-20592C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15378 AN: 151998 Hom.: 904 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.0617

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0973

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

GnomAD4 genome AF: 0.101 AC: 15390 AN: 152116 Hom.: 905 Cov.: 32 AF XY: 0.0993 AC XY: 7382 AN XY: 74372

African (AFR) AF: 0.0859 AC: 3566 AN: 41496

American (AMR) AF: 0.0731 AC: 1117 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3464

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4818

European-Finnish (FIN) AF: 0.150 AC: 1585 AN: 10568

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8635 AN: 67992

Other (OTH) AF: 0.0958 AC: 202 AN: 2108

Alfa AF: 0.110 Hom.: 169

Bravo AF: 0.0945

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.82
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11681243; hg19: chr2-48251156;