7-839130-T-G

Variant names:

• chr7-839130-T-G
• rs1127460
• NM_001130965.3:c.266+144T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001130965.3(SUN1):​c.266+144T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0000018 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SUN1 NM_001130965.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 7 publications found

Genes affected

SUN1 (HGNC:18587): (Sad1 and UNC84 domain containing 1) This gene is a member of the unc-84 homolog family and encodes a nuclear envelope protein with an Unc84 (SUN) domain. The protein is involved in nuclear anchorage and migration. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2019]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130965.3. 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
	SUN1	NM_001130965.3	MANE Select	c.266+144T>G		intron	N/A	NP_001124437.1	O94901-8
	SUN1	NM_001367651.1		c.485+144T>G		intron	N/A	NP_001354580.1
	SUN1	NM_001367705.1		c.266+144T>G		intron	N/A	NP_001354634.1	O94901-9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUN1	ENST00000401592.6	TSL:1 MANE Select	c.266+144T>G		intron	N/A	ENSP00000384015.1	O94901-8
	SUN1	ENST00000457378.6	TSL:1	c.329+144T>G		intron	N/A	ENSP00000395952.2	O94901-7
	SUN1	ENST00000963118.1		c.266+144T>G		intron	N/A	ENSP00000633177.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000178 AC: 1 AN: 560806 Hom.: 0 Cov.: 8 AF XY: 0.00000357 AC XY: 1 AN XY: 280402

African (AFR) AF: 0.0000737 AC: 1 AN: 13566

American (AMR) AF: 0.00 AC: 0 AN: 10458

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12576

East Asian (EAS) AF: 0.00 AC: 0 AN: 26184

South Asian (SAS) AF: 0.00 AC: 0 AN: 23896

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24810

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2006

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 419352

Other (OTH) AF: 0.00 AC: 0 AN: 27958

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 6198

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.41
PhyloP100		-0.085
PromoterAI		-0.010	Neutral

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: rs1127460; hg19: chr7-878767;