rs1512225

Variant names:

• chr2-60258458-C-T
• rs1512225
• ENST00000765305.1:n.154-7866G>A

Variant summary

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

The ENST00000765305.1(ENSG00000299640):​n.154-7866G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 152,260 control chromosomes in the GnomAD database, including 196 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 0.040 (196 hom., cov: 33)
• Consequence: ENSG00000299640 ENST00000765305.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 2 publications found

Genes affected

ENSG00000299640 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765305.1. 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
	ENSG00000299640	ENST00000765305.1		n.154-7866G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0402 AC: 6110 AN: 152142 Hom.: 196 Cov.: 33

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0168

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0402 AC: 6115 AN: 152260 Hom.: 196 Cov.: 33 AF XY: 0.0397 AC XY: 2959 AN XY: 74464

African (AFR) AF: 0.0779 AC: 3235 AN: 41530

American (AMR) AF: 0.0168 AC: 257 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.123 AC: 635 AN: 5180

South Asian (SAS) AF: 0.0255 AC: 123 AN: 4826

European-Finnish (FIN) AF: 0.0342 AC: 363 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0210 AC: 1427 AN: 68018

Other (OTH) AF: 0.0327 AC: 69 AN: 2112

Alfa AF: 0.0321 Hom.: 19

Bravo AF: 0.0406

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.054

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: rs1512225;

hg19: chr2-60485593;