rs4591358

Variant names:

• chr2-195501166-T-C
• rs4591358
• ENST00000606986.1:n.263+14271A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-195501166-T-C
• chr2-195501166-T-G

Variant summary

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

The ENST00000606986.1(ENSG00000271893):​n.263+14271A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,092 control chromosomes in the GnomAD database, including 8,225 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 0.33 (8225 hom., cov: 32)
• Consequence: ENSG00000271893 ENST00000606986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 4 publications found

Genes affected

ENSG00000271893 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 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
ENSG00000271893	ENST00000606986.1	n.263+14271A>G		intron_variant	Intron 1 of 2	3
ENSG00000271893	ENST00000760487.1	n.612-14386A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49783 AN: 151974 Hom.: 8221 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.327 AC: 49805 AN: 152092 Hom.: 8225 Cov.: 32 AF XY: 0.327 AC XY: 24314 AN XY: 74368

African (AFR) AF: 0.391 AC: 16204 AN: 41494

American (AMR) AF: 0.348 AC: 5320 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1361 AN: 5168

South Asian (SAS) AF: 0.276 AC: 1332 AN: 4828

European-Finnish (FIN) AF: 0.333 AC: 3512 AN: 10562

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20166 AN: 67962

Other (OTH) AF: 0.332 AC: 701 AN: 2114

Alfa AF: 0.305 Hom.: 19388

Bravo AF: 0.335

Asia WGS AF: 0.262 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.74
PhyloP100		0.082
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4591358; hg19: chr2-196365890;