chr7-93892898-G-A

Variant names:

• chr7-93892898-G-A
• rs3763473
• ENST00000455502.5:c.-12+6349G>A

Variant summary

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

The ENST00000455502.5(GNGT1):​c.-12+6349G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 152,078 control chromosomes in the GnomAD database, including 546 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 0.074 (546 hom., cov: 32)
• Consequence: GNGT1 ENST00000455502.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFPI2-DT	NR_134235.1	n.187-344G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNGT1	ENST00000455502.5	c.-12+6349G>A		intron_variant	Intron 2 of 3	2		ENSP00000395857.1
TFPI2-DT	ENST00000435257.2	n.257-344G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0737 AC: 11201 AN: 151960 Hom.: 543 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.0914

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0663

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

GnomAD4 genome AF: 0.0738 AC: 11228 AN: 152078 Hom.: 546 Cov.: 32 AF XY: 0.0749 AC XY: 5571 AN XY: 74348

African (AFR) AF: 0.116 AC: 4824 AN: 41472

American (AMR) AF: 0.117 AC: 1786 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3472

East Asian (EAS) AF: 0.170 AC: 877 AN: 5148

South Asian (SAS) AF: 0.0912 AC: 438 AN: 4800

European-Finnish (FIN) AF: 0.0291 AC: 308 AN: 10586

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0388 AC: 2641 AN: 68010

Other (OTH) AF: 0.0661 AC: 139 AN: 2102

Alfa AF: 0.0560 Hom.: 44

Bravo AF: 0.0802

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.31
PhyloP100		0.25
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: rs3763473; hg19: chr7-93522210;