3-63626755-T-C

Variant names:

• chr3-63626755-T-C
• rs7646765
• ENST00000803954.1:n.123+18760A>G

Variant summary

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

The ENST00000803954.1(SYNPR-AS1):​n.123+18760A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,996 control chromosomes in the GnomAD database, including 23,369 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 0.55 (23369 hom., cov: 32)
• Consequence: SYNPR-AS1 ENST00000803954.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 1 publications found

Genes affected

SYNPR-AS1 (HGNC:40774): (SYNPR antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803954.1. 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
	SYNPR-AS1	ENST00000803954.1		n.123+18760A>G		intron	N/A
	SYNPR-AS1	ENST00000803955.1		n.74+18760A>G		intron	N/A
	SYNPR-AS1	ENST00000803956.1		n.80+18760A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83216 AN: 151878 Hom.: 23323 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.548 AC: 83328 AN: 151996 Hom.: 23369 Cov.: 32 AF XY: 0.544 AC XY: 40401 AN XY: 74274

African (AFR) AF: 0.672 AC: 27859 AN: 41470

American (AMR) AF: 0.465 AC: 7100 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3470

East Asian (EAS) AF: 0.561 AC: 2880 AN: 5136

South Asian (SAS) AF: 0.534 AC: 2569 AN: 4810

European-Finnish (FIN) AF: 0.472 AC: 4988 AN: 10572

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.505 AC: 34294 AN: 67954

Other (OTH) AF: 0.536 AC: 1133 AN: 2114

Alfa AF: 0.523 Hom.: 60979

Bravo AF: 0.554

Asia WGS AF: 0.565 AC: 1964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.8
DANN	Benign	0.73
PhyloP100		-0.27

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: rs7646765;

hg19: chr3-63612431;