8-73009299-G-GGAGGTCGGGAGA

Position:

• chr8-73009299-G-GGAGGTCGGGAGA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017489.3(TERF1):​c.319+98_319+99insTCGGGAGAGAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.99 (75038 hom., cov: 0)
  • Exomes 𝑓: 0.99 (570658 hom.)
  • Failed GnomAD Quality Control
• Consequence: TERF1 NM_017489.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.560

Genes affected

TERF1 (HGNC:11728): (telomeric repeat binding factor 1) This gene encodes a telomere specific protein which is a component of the telomere nucleoprotein complex. This protein is present at telomeres throughout the cell cycle and functions as an inhibitor of telomerase, acting in cis to limit the elongation of individual chromosome ends. The protein structure contains a C-terminal Myb motif, a dimerization domain near its N-terminus and an acidic N-terminus. Multiple transcripts of this gene are alternatively spliced products. [provided by RefSeq, Aug 2022]

TERF1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-73009299-G-GGAGGTCGGGAGA is Benign according to our data. Variant chr8-73009299-G-GGAGGTCGGGAGA is described in ClinVar as [Benign]. Clinvar id is 1260888.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TERF1	NM_017489.3	c.319+98_319+99insTCGGGAGAGAGG		intron_variant		ENST00000276603.10	NP_059523.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TERF1	ENST00000276603.10	c.319+98_319+99insTCGGGAGAGAGG		intron_variant		1	NM_017489.3	ENSP00000276603.5

Frequencies

GnomAD3 genomes AF: 0.993 AC: 150995 AN: 152048 Hom.: 74980 Cov.: 0

Gnomad AFR AF: 0.998

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.996

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.994

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.989 AC: 1153964 AN: 1167048 Hom.: 570658 Cov.: 18 AF XY: 0.989 AC XY: 571074 AN XY: 577438

Gnomad4 AFR exome AF: 0.998

Gnomad4 AMR exome AF: 0.998

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.995

Gnomad4 FIN exome AF: 0.996

Gnomad4 NFE exome AF: 0.987

Gnomad4 OTH exome AF: 0.989

GnomAD4 genome AF: 0.993 AC: 151111 AN: 152164 Hom.: 75038 Cov.: 0 AF XY: 0.994 AC XY: 73897 AN XY: 74372

Gnomad4 AFR AF: 0.998

Gnomad4 AMR AF: 0.996

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.996

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.994

Alfa AF: 0.989 Hom.: 2187

Asia WGS AF: 0.998 AC: 3470 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 15, 2019

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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: rs71267925; hg19: chr8-73921534;