rs4791362

chr17-9810769-G-A

Variant summary

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

The NM_001310219.2(GSG1L2):c.311-151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 631,666 control chromosomes in the GnomAD database, including 18,041 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 0.22 (3951 hom., cov: 32)
  • Exomes 𝑓: 0.23 (14090 hom.)
• Consequence: GSG1L2 NM_001310219.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

Genes affected

GSG1L2 (HGNC:51826): (GSG1 like 2) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSG1L2	NM_001310219.2	c.311-151C>T		intron_variant		ENST00000399363.5
LOC124903925	XR_007065616.1	n.2420G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSG1L2	ENST00000399363.5	c.311-151C>T		intron_variant		5	NM_001310219.2	P1
	ENST00000635215.1	n.2606G>A		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33640 AN: 151876 Hom.: 3949 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.229 AC: 109934 AN: 479672 Hom.: 14090 Cov.: 0 AF XY: 0.233 AC XY: 59510 AN XY: 255712

Gnomad4 AFR exome AF: 0.221

Gnomad4 AMR exome AF: 0.351

Gnomad4 ASJ exome AF: 0.176

Gnomad4 EAS exome AF: 0.384

Gnomad4 SAS exome AF: 0.322

Gnomad4 FIN exome AF: 0.289

Gnomad4 NFE exome AF: 0.183

Gnomad4 OTH exome AF: 0.218

GnomAD4 genome AF: 0.222 AC: 33667 AN: 151994 Hom.: 3951 Cov.: 32 AF XY: 0.230 AC XY: 17049 AN XY: 74254

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.216

Alfa AF: 0.196 Hom.: 4290

Bravo AF: 0.223

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.8
Dann	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4791362; hg19: chr17-9714086; COSMIC: COSV68010501; COSMIC: COSV68010501;