7-48012082-G-T

Variant names:

• chr7-48012082-G-T
• rs2708909
• NM_001030019.2:c.289-3007C>A

Variant summary

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

The NM_001030019.2(SUN3):​c.289-3007C>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
• Publications: 10 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001030019.2. 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
	SUN3	NM_001030019.2	MANE Select	c.289-3007C>A		intron	N/A	NP_001025190.1	Q8TAQ9-1
	SUN3	NM_152782.4		c.289-3007C>A		intron	N/A	NP_689995.3
	SUN3	NM_001284350.2		c.253-3007C>A		intron	N/A	NP_001271279.1	Q8TAQ9-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUN3	ENST00000297325.9	TSL:5 MANE Select	c.289-3007C>A		intron	N/A	ENSP00000297325.4	Q8TAQ9-1
	SUN3	ENST00000395572.6	TSL:1	c.289-3007C>A		intron	N/A	ENSP00000378939.2	Q8TAQ9-1
	SUN3	ENST00000412142.5	TSL:5	c.253-3007C>A		intron	N/A	ENSP00000410204.2	Q8TAQ9-3

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

African (AFR) AF: 0.239 AC: 9926 AN: 41510

American (AMR) AF: 0.463 AC: 7073 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2173 AN: 5176

South Asian (SAS) AF: 0.356 AC: 1715 AN: 4818

European-Finnish (FIN) AF: 0.564 AC: 5970 AN: 10576

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34380 AN: 67974

Other (OTH) AF: 0.396 AC: 833 AN: 2106

Alfa AF: 0.480 Hom.: 16049

Bravo AF: 0.405

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.69
PhyloP100		-0.13
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: rs2708909; hg19: chr7-48051679;