2-48156607-G-T

Variant names:

• chr2-48156607-G-T
• rs7570354
• ENST00000447571.5:n.240+8281C>A

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.240+8281C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,734 control chromosomes in the GnomAD database, including 20,914 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 0.51 (20914 hom., cov: 30)
• Consequence: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230773	ENST00000447571.5	TSL:1	n.240+8281C>A		intron	N/A
	ENSG00000230773	ENST00000587616.1	TSL:5	n.47+8281C>A		intron	N/A
	ENSG00000230773	ENST00000649883.1		n.68-7499C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77179 AN: 151616 Hom.: 20911 Cov.: 30

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.509 AC: 77230 AN: 151734 Hom.: 20914 Cov.: 30 AF XY: 0.514 AC XY: 38105 AN XY: 74136

African (AFR) AF: 0.612 AC: 25321 AN: 41374

American (AMR) AF: 0.503 AC: 7666 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1875 AN: 3470

East Asian (EAS) AF: 0.954 AC: 4921 AN: 5160

South Asian (SAS) AF: 0.714 AC: 3421 AN: 4788

European-Finnish (FIN) AF: 0.353 AC: 3709 AN: 10498

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28603 AN: 67890

Other (OTH) AF: 0.500 AC: 1055 AN: 2110

Alfa AF: 0.461 Hom.: 50346

Bravo AF: 0.524

Asia WGS AF: 0.808 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7570354; hg19: chr2-48383746;