ENST00000421143.7:n.362-37782C>A

Variant names:

• chr20-10064430-G-T
• rs674630
• ENST00000421143.7:n.362-37782C>A

Variant summary

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

The ENST00000421143.7(SNAP25-AS1):​n.362-37782C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,936 control chromosomes in the GnomAD database, including 20,010 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 0.51 (20010 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000421143.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 8 publications found

Genes affected

SNAP25-AS1 (HGNC:44312): (SNAP25 antisense RNA 1)

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 (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNAP25-AS1	NR_040710.1	n.500-37782C>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNAP25-AS1	ENST00000421143.7	n.362-37782C>A		intron_variant	Intron 3 of 3	5
SNAP25-AS1	ENST00000603542.6	n.748-37782C>A		intron_variant	Intron 3 of 4	2
SNAP25-AS1	ENST00000655307.1	n.629-37782C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77369 AN: 151818 Hom.: 19993 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.510 AC: 77429 AN: 151936 Hom.: 20010 Cov.: 32 AF XY: 0.508 AC XY: 37734 AN XY: 74252

African (AFR) AF: 0.458 AC: 18972 AN: 41410

American (AMR) AF: 0.486 AC: 7416 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3472

East Asian (EAS) AF: 0.270 AC: 1396 AN: 5162

South Asian (SAS) AF: 0.450 AC: 2164 AN: 4808

European-Finnish (FIN) AF: 0.585 AC: 6166 AN: 10546

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38128 AN: 67954

Other (OTH) AF: 0.493 AC: 1040 AN: 2110

Alfa AF: 0.544 Hom.: 38179

Bravo AF: 0.502

Asia WGS AF: 0.343 AC: 1195 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	3.5
DANN	Benign	0.77
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs674630; hg19: chr20-10045078;