chr9-133330998-A-G

Variant names:

• chr9-133330998-A-G
• rs12335
• NM_006753.6:c.*871T>C

Variant summary

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

The NM_006753.6(SURF6):​c.*871T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,030 control chromosomes in the GnomAD database, including 21,588 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 0.53 (21587 hom., cov: 32)
  • Exomes 𝑓: 0.58 (1 hom.)
• Consequence: SURF6 NM_006753.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978
• Publications: 25 publications found

Genes affected

SURF6 (HGNC:11478): (surfeit 6) This gene encodes a conserved protein that is localized to the nucleolus. The encoded protein may function as a nucleolar-matrix protein with nucleic acid-binding properties. There is a pseudogene for this gene on chromosome Y. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006753.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SURF6	NM_006753.6	MANE Select	c.*871T>C		3_prime_UTR	Exon 5 of 5	NP_006744.2
	SURF6	NR_103874.2		n.1960T>C		non_coding_transcript_exon	Exon 5 of 5
	SURF6	NM_001278942.2		c.*1362T>C		3_prime_UTR	Exon 5 of 5	NP_001265871.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SURF6	ENST00000372022.6	TSL:1 MANE Select	c.*871T>C		3_prime_UTR	Exon 5 of 5	ENSP00000361092.4

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80350 AN: 151900 Hom.: 21553 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.484

GnomAD4 exome AF: 0.583 AC: 7 AN: 12 Hom.: 1 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.625 AC: 5 AN: 8

GnomAD4 genome AF: 0.529 AC: 80432 AN: 152018 Hom.: 21587 Cov.: 32 AF XY: 0.531 AC XY: 39472 AN XY: 74296

African (AFR) AF: 0.584 AC: 24217 AN: 41456

American (AMR) AF: 0.462 AC: 7065 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1767 AN: 5168

South Asian (SAS) AF: 0.510 AC: 2455 AN: 4818

European-Finnish (FIN) AF: 0.604 AC: 6376 AN: 10558

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35589 AN: 67946

Other (OTH) AF: 0.481 AC: 1015 AN: 2112

Alfa AF: 0.520 Hom.: 5653

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs12335; hg19: chr9-136197834;