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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762203.1. 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
	ENSG00000299281	ENST00000762203.1		n.108+28860C>T		intron	N/A
	ENSG00000299281	ENST00000762204.1		n.129-2875C>T		intron	N/A
	ENSG00000299281	ENST00000762205.1		n.225-2875C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1453160;

hg19: chr2-207877465;