7-48004881-C-T

Variant names:

• chr7-48004881-C-T
• rs1915960
• NM_001030019.2:c.577+1088G>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.577+1088G>A 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 152,148 control chromosomes in the GnomAD database, including 9,480 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 (9480 hom., cov: 33)
• Consequence: SUN3 NM_001030019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 11 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=-0.92).
• 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.577+1088G>A		intron_variant	Intron 6 of 9	ENST00000297325.9	NP_001025190.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUN3	ENST00000297325.9	c.577+1088G>A		intron_variant	Intron 6 of 9	5	NM_001030019.2	ENSP00000297325.4

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50798 AN: 152032 Hom.: 9478 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.415

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: 50804 AN: 152148 Hom.: 9480 Cov.: 33 AF XY: 0.333 AC XY: 24747 AN XY: 74390

African (AFR) AF: 0.161 AC: 6667 AN: 41524

American (AMR) AF: 0.363 AC: 5546 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1391 AN: 5176

South Asian (SAS) AF: 0.455 AC: 2195 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3758 AN: 10580

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

European-Non Finnish (NFE) AF: 0.415 AC: 28240 AN: 67976

Other (OTH) AF: 0.392 AC: 830 AN: 2116

Alfa AF: 0.393 Hom.: 53220

Bravo AF: 0.329

Asia WGS AF: 0.340 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.23
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: rs1915960; hg19: chr7-48044478;