chr7-48012082-G-T

Position:

• chr7-48012082-G-T

Variant summary

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

The NM_001030019.2(SUN3):​c.289-3007C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,120 control chromosomes in the GnomAD database, including 14,598 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 0.42 (14598 hom., cov: 33)
• Consequence: SUN3 NM_001030019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

SUN3 (HGNC:22429): (Sad1 and UNC84 domain containing 3) Predicted to enable protein-membrane adaptor activity. Predicted to be involved in nuclear envelope organization. Predicted to be integral component of nuclear inner membrane. Predicted to be part of meiotic nuclear membrane microtubule tethering complex. Predicted to be active in nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUN3	NM_001030019.2	c.289-3007C>A		intron_variant		ENST00000297325.9	NP_001025190.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUN3	ENST00000297325.9	c.289-3007C>A		intron_variant		5	NM_001030019.2	ENSP00000297325.4

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63969 AN: 152002 Hom.: 14594 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.421 AC: 63976 AN: 152120 Hom.: 14598 Cov.: 33 AF XY: 0.424 AC XY: 31490 AN XY: 74340

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.396

Alfa AF: 0.481 Hom.: 12596

Bravo AF: 0.405

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2708909; hg19: chr7-48051679;