rs1517440

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414512.1(ENSG00000236451):​n.369-41226T>C variant causes a intron, non coding transcript 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: ENST00000414512.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105373895	XR_923937.3	n.184+20524T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000414512.1	n.369-41226T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000665624.1	n.476+20524T>C		intron_variant, non_coding_transcript_variant
	ENST00000670511.1	n.748+20524T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00921

Gnomad4 AMR AF: 0.0597

Gnomad4 ASJ AF: 0.0800

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.0756

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.0477

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0310 Hom.: 33

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517440; hg19: chr2-221453874;