ENST00000510972.5:n.303+10763G>C

Variant names:

• chr5-122467823-C-G
• rs11241644
• ENST00000510972.5:n.303+10763G>C

Variant summary

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

The ENST00000510972.5(MGC32805):​n.303+10763G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,190 control chromosomes in the GnomAD database, including 3,473 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 0.20 (3473 hom., cov: 32)
• Consequence: MGC32805 ENST00000510972.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 3 publications found

Genes affected

MGC32805 (HGNC:28478):

LOC107986446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNCAIP-AS3	NR_051996.1	n.303+10763G>C		intron_variant	Intron 2 of 5
LOC107986446	XR_001742867.2	n.118+1161G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MGC32805	ENST00000510972.5	n.303+10763G>C		intron_variant	Intron 2 of 5	1
MGC32805	ENST00000721146.1	n.597G>C		non_coding_transcript_exon_variant	Exon 5 of 5
MGC32805	ENST00000721147.1	n.495G>C		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29876 AN: 152072 Hom.: 3467 Cov.: 32

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.196 AC: 29891 AN: 152190 Hom.: 3473 Cov.: 32 AF XY: 0.202 AC XY: 14999 AN XY: 74408

African (AFR) AF: 0.0776 AC: 3223 AN: 41556

American (AMR) AF: 0.247 AC: 3779 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1472 AN: 5174

South Asian (SAS) AF: 0.305 AC: 1473 AN: 4828

European-Finnish (FIN) AF: 0.290 AC: 3064 AN: 10572

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15568 AN: 67996

Other (OTH) AF: 0.193 AC: 407 AN: 2108

Alfa AF: 0.224 Hom.: 527

Bravo AF: 0.185

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs11241644; hg19: chr5-121803518;