rs60215632

Positions:

• chr7-93892266-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134235.1(TFPI2-DT):​n.187-976T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 152,194 control chromosomes in the GnomAD database, including 436 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 0.060 (436 hom., cov: 32)
• Consequence: TFPI2-DT NR_134235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

Genes affected

TFPI2-DT (HGNC:40581): (TFPI2 divergent transcript)

GNGT1 (HGNC:4411): (G protein subunit gamma transducin 1) This gene encodes the gamma subunit of transducin, a guanine nucleotide-binding protein (G protein) that is found in rod outer segments. Transducin, also known as GMPase, mediates the activation of a cyclic GTP-specific (guanosine monophosphate) phosphodiesterase by rhodopsin. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TFPI2-DT	NR_134235.1	n.187-976T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TFPI2-DT	ENST00000435257.1	n.168-976T>G		intron_variant, non_coding_transcript_variant		2
GNGT1	ENST00000455502.5	c.-12+5717T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0602 AC: 9161 AN: 152076 Hom.: 434 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0570

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0603 AC: 9181 AN: 152194 Hom.: 436 Cov.: 32 AF XY: 0.0627 AC XY: 4669 AN XY: 74414

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0859

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0187

Gnomad4 OTH AF: 0.0569

Alfa AF: 0.0374 Hom.: 23

Bravo AF: 0.0663

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60215632; hg19: chr7-93521578;