17-9806629-G-A

Position:

• chr17-9806629-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.623+861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,974 control chromosomes in the GnomAD database, including 18,300 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 0.49 (18300 hom., cov: 32)
• Consequence: GSG1L2 NM_001310219.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSG1L2	NM_001310219.2	c.623+861C>T		intron_variant		ENST00000399363.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSG1L2	ENST00000399363.5	c.623+861C>T		intron_variant		5	NM_001310219.2	P1
	ENST00000635215.1	n.187-832G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74393 AN: 151856 Hom.: 18294 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.490 AC: 74442 AN: 151974 Hom.: 18300 Cov.: 32 AF XY: 0.491 AC XY: 36423 AN XY: 74256

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.495

Alfa AF: 0.467 Hom.: 34568

Bravo AF: 0.494

Asia WGS AF: 0.498 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.26

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: rs9914518; hg19: chr17-9709946;