15-22460870-C-T

Variant names:

• chr15-22460870-C-T
• rs527945774
• NM_001396956.1:c.231C>T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001396956.1(GOLGA6L22):​c.231C>T​(p.Ser77Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00056 (2 hom., cov: 19)
  • Exomes 𝑓: 0.00027 (23 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L22 NM_001396956.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.784

Genes affected

GOLGA6L22 (HGNC:50289): (golgin A6 family like 22)

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 15-22460870-C-T is Benign according to our data. Variant chr15-22460870-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644966.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.784 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L22	NM_001396956.1	c.231C>T	p.Ser77Ser	synonymous_variant	Exon 2 of 9	ENST00000622895.2	NP_001383885.1
GOLGA6L22	NM_001396957.1	c.231C>T	p.Ser77Ser	synonymous_variant	Exon 2 of 9		NP_001383886.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6L22	ENST00000622895.2	c.231C>T	p.Ser77Ser	synonymous_variant	Exon 2 of 9	5	NM_001396956.1	ENSP00000483673.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 73 AN: 130910 Hom.: 2 Cov.: 19 FAILED QC

Gnomad AFR AF: 0.000166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000230

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.000489

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000793

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000268 AC: 375 AN: 1397030 Hom.: 23 Cov.: 30 AF XY: 0.000253 AC XY: 176 AN XY: 694664

Gnomad4 AFR exome AF: 0.000136

Gnomad4 AMR exome AF: 0.0000237

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00743

Gnomad4 SAS exome AF: 0.000172

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000337

Gnomad4 OTH exome AF: 0.000488

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000557 AC: 73 AN: 130976 Hom.: 2 Cov.: 19 AF XY: 0.000549 AC XY: 35 AN XY: 63810

Gnomad4 AFR AF: 0.000166

Gnomad4 AMR AF: 0.000230

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.000489

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000793

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000164 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

RP11-467N20.5: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.32

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: rs527945774; hg19: chr15-22738231;