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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374593	XR_001739456.2	n.397+8281C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230773	ENST00000447571.5	n.240+8281C>A		intron_variant	Intron 3 of 8	1
ENSG00000230773	ENST00000587616.1	n.47+8281C>A		intron_variant	Intron 1 of 10	5
ENSG00000230773	ENST00000649883.1	n.68-7499C>A		intron_variant	Intron 2 of 8

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 v4.3

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;