rs2358462

Variant names:

• chr4-148649528-T-C
• rs2358462
• ENST00000661928.1:n.222+104944T>C

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.222+104944T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,038 control chromosomes in the GnomAD database, including 10,552 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 0.36 (10552 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 8 publications found

Genes affected

ENSG00000287292 (HGNC:58892):

LOC107986195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661928.1. 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
	ENSG00000287292	ENST00000661928.1		n.222+104944T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54779 AN: 151918 Hom.: 10546 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.360 AC: 54806 AN: 152038 Hom.: 10552 Cov.: 32 AF XY: 0.355 AC XY: 26360 AN XY: 74306

African (AFR) AF: 0.252 AC: 10449 AN: 41470

American (AMR) AF: 0.282 AC: 4307 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1250 AN: 3464

East Asian (EAS) AF: 0.245 AC: 1270 AN: 5184

South Asian (SAS) AF: 0.312 AC: 1499 AN: 4808

European-Finnish (FIN) AF: 0.371 AC: 3923 AN: 10566

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30834 AN: 67960

Other (OTH) AF: 0.356 AC: 748 AN: 2104

Alfa AF: 0.413 Hom.: 31052

Bravo AF: 0.347

Asia WGS AF: 0.292 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.90
PhyloP100		0.33

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: rs2358462;

hg19: chr4-149570680;