rs60215632

Variant names:

• chr7-93892266-T-G
• rs60215632
• ENST00000455502.5:c.-12+5717T>G

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-12+5717T>G variant causes a intron 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: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 1 publications found

Genes affected

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]

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455502.5. 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
	TFPI2-DT	NR_134235.1		n.187-976T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNGT1	ENST00000455502.5	TSL:2	c.-12+5717T>G		intron	N/A	ENSP00000395857.1
	TFPI2-DT	ENST00000435257.2	TSL:2	n.257-976T>G		intron	N/A

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

African (AFR) AF: 0.105 AC: 4374 AN: 41512

American (AMR) AF: 0.107 AC: 1642 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3472

East Asian (EAS) AF: 0.170 AC: 877 AN: 5168

South Asian (SAS) AF: 0.0859 AC: 414 AN: 4822

European-Finnish (FIN) AF: 0.0256 AC: 271 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0187 AC: 1273 AN: 68014

Other (OTH) AF: 0.0569 AC: 120 AN: 2108

Alfa AF: 0.0404 Hom.: 30

Bravo AF: 0.0663

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.5
DANN	Benign	0.54
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs60215632; hg19: chr7-93521578;