rs1453160

Variant names:

• chr2-207012741-G-A
• rs1453160
• ENST00000762203.1:n.108+28860C>T

Variant summary

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

The ENST00000762203.1(ENSG00000299281):​n.108+28860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,170 control chromosomes in the GnomAD database, including 1,900 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 0.15 (1900 hom., cov: 32)
• Consequence: ENSG00000299281 ENST00000762203.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 4 publications found

Genes affected

ENSG00000299281 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299281	ENST00000762203.1	n.108+28860C>T		intron_variant	Intron 1 of 1
ENSG00000299281	ENST00000762204.1	n.129-2875C>T		intron_variant	Intron 1 of 1
ENSG00000299281	ENST00000762205.1	n.225-2875C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23481 AN: 152052 Hom.: 1898 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0738

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.154 AC: 23500 AN: 152170 Hom.: 1900 Cov.: 32 AF XY: 0.154 AC XY: 11420 AN XY: 74388

African (AFR) AF: 0.195 AC: 8097 AN: 41496

American (AMR) AF: 0.125 AC: 1919 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3470

East Asian (EAS) AF: 0.152 AC: 788 AN: 5178

South Asian (SAS) AF: 0.0855 AC: 412 AN: 4820

European-Finnish (FIN) AF: 0.130 AC: 1376 AN: 10598

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9878 AN: 68000

Other (OTH) AF: 0.168 AC: 355 AN: 2108

Alfa AF: 0.148 Hom.: 1006

Bravo AF: 0.156

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.36
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1453160; hg19: chr2-207877465;