rs12617311

Variant names:

• chr2-198767841-G-A
• rs12617311
• ENST00000440609.1:n.98+4418C>T

Variant summary

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

The ENST00000440609.1(ENSG00000225421):​n.98+4418C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,784 control chromosomes in the GnomAD database, including 6,607 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 0.28 (6607 hom., cov: 30)
• Consequence: ENSG00000225421 ENST00000440609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 29 publications found

Genes affected

ENSG00000225421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440609.1. 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
	ENSG00000225421	ENST00000440609.1	TSL:4	n.98+4418C>T		intron	N/A
	ENSG00000225421	ENST00000748012.1		n.25+4418C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42947 AN: 151666 Hom.: 6606 Cov.: 30

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.283 AC: 42973 AN: 151784 Hom.: 6607 Cov.: 30 AF XY: 0.285 AC XY: 21159 AN XY: 74150

African (AFR) AF: 0.158 AC: 6542 AN: 41428

American (AMR) AF: 0.307 AC: 4677 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2068 AN: 5120

South Asian (SAS) AF: 0.463 AC: 2221 AN: 4796

European-Finnish (FIN) AF: 0.284 AC: 2994 AN: 10532

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22191 AN: 67886

Other (OTH) AF: 0.301 AC: 635 AN: 2112

Alfa AF: 0.318 Hom.: 28012

Bravo AF: 0.281

Asia WGS AF: 0.407 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.16

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: rs12617311;

hg19: chr2-199632565;