chr2-48205782-T-C

Variant names:

• chr2-48205782-T-C
• rs13431982
• ENST00000447571.5:n.57-25324A>G

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.57-25324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,064 control chromosomes in the GnomAD database, including 3,634 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 0.18 (3634 hom., cov: 32)
• Consequence: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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.57-25324A>G		intron	N/A
	ENSG00000230773	ENST00000650704.1		n.290+37687A>G		intron	N/A
	ENSG00000230773	ENST00000651429.1		n.169-40848A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27714 AN: 151946 Hom.: 3620 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.183 AC: 27764 AN: 152064 Hom.: 3634 Cov.: 32 AF XY: 0.179 AC XY: 13304 AN XY: 74358

African (AFR) AF: 0.365 AC: 15113 AN: 41420

American (AMR) AF: 0.107 AC: 1635 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.0174 AC: 84 AN: 4824

European-Finnish (FIN) AF: 0.148 AC: 1566 AN: 10580

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.130 AC: 8808 AN: 67994

Other (OTH) AF: 0.154 AC: 326 AN: 2112

Alfa AF: 0.128 Hom.: 1089

Bravo AF: 0.188

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.017
DANN	Benign	0.31
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs13431982; hg19: chr2-48432921;