chr7-93891949-G-C

Variant names:

• chr7-93891949-G-C
• rs59805398
• ENST00000455502.5:c.-12+5400G>C

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-12+5400G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,034 control chromosomes in the GnomAD database, including 6,306 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 0.27 (6306 hom., cov: 32)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 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.186+870G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNGT1	ENST00000455502.5	TSL:2	c.-12+5400G>C		intron	N/A	ENSP00000395857.1
	TFPI2-DT	ENST00000435257.2	TSL:2	n.256+870G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41386 AN: 151916 Hom.: 6302 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.272 AC: 41416 AN: 152034 Hom.: 6306 Cov.: 32 AF XY: 0.283 AC XY: 21004 AN XY: 74322

African (AFR) AF: 0.205 AC: 8499 AN: 41472

American (AMR) AF: 0.373 AC: 5700 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 744 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3161 AN: 5162

South Asian (SAS) AF: 0.389 AC: 1874 AN: 4820

European-Finnish (FIN) AF: 0.332 AC: 3499 AN: 10542

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17048 AN: 67966

Other (OTH) AF: 0.299 AC: 631 AN: 2112

Alfa AF: 0.257 Hom.: 642

Bravo AF: 0.275

Asia WGS AF: 0.472 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.96
DANN	Benign	0.72
PhyloP100		-0.47
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: rs59805398; hg19: chr7-93521261;