chr7-48012953-T-C

Variant names:

• chr7-48012953-T-C
• rs11772387
• NM_001030019.2:c.289-3878A>G

Variant summary

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

The NM_001030019.2(SUN3):​c.289-3878A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,118 control chromosomes in the GnomAD database, including 9,531 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 0.33 (9531 hom., cov: 32)
• Consequence: SUN3 NM_001030019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 6 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUN3	NM_001030019.2	c.289-3878A>G		intron_variant	Intron 3 of 9	ENST00000297325.9	NP_001025190.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUN3	ENST00000297325.9	c.289-3878A>G		intron_variant	Intron 3 of 9	5	NM_001030019.2	ENSP00000297325.4

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50825 AN: 151998 Hom.: 9528 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.334 AC: 50837 AN: 152118 Hom.: 9531 Cov.: 32 AF XY: 0.333 AC XY: 24789 AN XY: 74366

African (AFR) AF: 0.157 AC: 6511 AN: 41534

American (AMR) AF: 0.363 AC: 5552 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1547 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1563 AN: 5166

South Asian (SAS) AF: 0.456 AC: 2201 AN: 4830

European-Finnish (FIN) AF: 0.356 AC: 3765 AN: 10564

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28236 AN: 67946

Other (OTH) AF: 0.393 AC: 829 AN: 2110

Alfa AF: 0.406 Hom.: 23464

Bravo AF: 0.330

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.47
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11772387; hg19: chr7-48052550;