9-133356757-CAGGGGAG-C

Position:

• chr9-133356757-CAGGGGAG-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_017503.5(SURF2):​c.78+104_78+110delGGGAGAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0275 in 1,339,896 control chromosomes in the GnomAD database, including 705 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.034 (78 hom., cov: 28)
  • Exomes 𝑓: 0.027 (627 hom.)
• Consequence: SURF2 NM_017503.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0640

Genes affected

SURF2 (HGNC:11475): (surfeit 2) This gene shares a bidirectional promoter with surfeit 1 (SURF1; GeneID: 6834), which is located on the opposite strand. It encodes a conserved protein that is expressed in a variety of tissues. [provided by RefSeq, Jul 2013]

SURF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 9-133356757-CAGGGGAG-C is Benign according to our data. Variant chr9-133356757-CAGGGGAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 1218470.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0341 (4797/140844) while in subpopulation NFE AF= 0.0352 (2279/64758). AF 95% confidence interval is 0.034. There are 78 homozygotes in gnomad4. There are 2287 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 78 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SURF2	NM_017503.5	c.78+104_78+110delGGGAGAG		intron_variant		ENST00000371964.5	NP_059973.4
SURF2	NM_001278928.2	c.78+104_78+110delGGGAGAG		intron_variant			NP_001265857.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SURF2	ENST00000371964.5	c.78+104_78+110delGGGAGAG		intron_variant		1	NM_017503.5	ENSP00000361032.4
SURF2	ENST00000495524.5	n.93+104_93+110delGGGAGAG		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0341 AC: 4798 AN: 140788 Hom.: 78 Cov.: 28

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0342

Gnomad ASJ AF: 0.0707

Gnomad EAS AF: 0.000610

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.0197

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0397

GnomAD4 exome AF: 0.0267 AC: 32015 AN: 1199052 Hom.: 627 AF XY: 0.0266 AC XY: 15549 AN XY: 584666

Gnomad4 AFR exome AF: 0.0265

Gnomad4 AMR exome AF: 0.0224

Gnomad4 ASJ exome AF: 0.0592

Gnomad4 EAS exome AF: 0.000698

Gnomad4 SAS exome AF: 0.0136

Gnomad4 FIN exome AF: 0.0295

Gnomad4 NFE exome AF: 0.0278

Gnomad4 OTH exome AF: 0.0269

GnomAD4 genome AF: 0.0341 AC: 4797 AN: 140844 Hom.: 78 Cov.: 28 AF XY: 0.0335 AC XY: 2287 AN XY: 68174

Gnomad4 AFR AF: 0.0318

Gnomad4 AMR AF: 0.0342

Gnomad4 ASJ AF: 0.0707

Gnomad4 EAS AF: 0.000612

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.0432

Gnomad4 NFE AF: 0.0352

Gnomad4 OTH AF: 0.0393

Bravo AF: 0.0336

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 26, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs587680893; hg19: chr9-136223633;