rs1517440

Variant names:

• chr2-220589153-T-C
• rs1517440
• ENST00000414512.1:n.369-41226T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-220589153-T-C
• chr2-220589153-T-G

Variant summary

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

The ENST00000414512.1(ENSG00000288902):​n.369-41226T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0394 in 152,118 control chromosomes in the GnomAD database, including 166 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 0.039 (166 hom., cov: 32)
• Consequence: ENSG00000288902 ENST00000414512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 4 publications found

Genes affected

ENSG00000288902 (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 (SAS) allele frequency at 95% confidence interval = 0.0692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373895	XR_923937.3	n.184+20524T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288902	ENST00000414512.1	n.369-41226T>C		intron_variant	Intron 1 of 4	1
ENSG00000288902	ENST00000665624.1	n.476+20524T>C		intron_variant	Intron 2 of 3
ENSG00000288902	ENST00000670511.1	n.748+20524T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5983 AN: 152000 Hom.: 164 Cov.: 32

Gnomad AFR AF: 0.00921

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0800

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0394 AC: 5989 AN: 152118 Hom.: 166 Cov.: 32 AF XY: 0.0404 AC XY: 3000 AN XY: 74342

African (AFR) AF: 0.00921 AC: 382 AN: 41498

American (AMR) AF: 0.0597 AC: 910 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0800 AC: 277 AN: 3464

East Asian (EAS) AF: 0.0645 AC: 334 AN: 5178

South Asian (SAS) AF: 0.0756 AC: 364 AN: 4812

European-Finnish (FIN) AF: 0.0293 AC: 311 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0477 AC: 3242 AN: 67996

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0377 Hom.: 63

Bravo AF: 0.0389

Asia WGS AF: 0.0830 AC: 289 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	1.5
DANN	Benign	0.40
PhyloP100		-0.023
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: rs1517440; hg19: chr2-221453874;