rs4791362

Variant names:

• chr17-9810769-G-A
• rs4791362
• NM_001310219.2:c.311-151C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000283025 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001310219.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSG1L2	NM_001310219.2	MANE Select	c.311-151C>T		intron	N/A	NP_001297148.1	A8MUP6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSG1L2	ENST00000399363.5	TSL:5 MANE Select	c.311-151C>T		intron	N/A	ENSP00000465978.1	A8MUP6
	ENSG00000283025	ENST00000635215.1	TSL:5	n.2606G>A		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.221 AC: 3005 AN: 13600

American (AMR) AF: 0.351 AC: 8870 AN: 25264

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 2667 AN: 15130

East Asian (EAS) AF: 0.384 AC: 12113 AN: 31510

South Asian (SAS) AF: 0.322 AC: 15833 AN: 49112

European-Finnish (FIN) AF: 0.289 AC: 8828 AN: 30548

Middle Eastern (MID) AF: 0.178 AC: 389 AN: 2190

European-Non Finnish (NFE) AF: 0.183 AC: 52249 AN: 284908

Other (OTH) AF: 0.218 AC: 5980 AN: 27410

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

African (AFR) AF: 0.225 AC: 9311 AN: 41456

American (AMR) AF: 0.283 AC: 4329 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1895 AN: 5156

South Asian (SAS) AF: 0.325 AC: 1562 AN: 4808

European-Finnish (FIN) AF: 0.304 AC: 3201 AN: 10530

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12105 AN: 67980

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.198 Hom.: 5566

Bravo AF: 0.223

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.55
PhyloP100		0.31

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

Other links and lift over

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