rs989100

Positions:

• chr7-127580864-T-C

Variant summary

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

The NM_024523.6(GCC1):​c.*1150A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,242 control chromosomes in the GnomAD database, including 3,859 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 0.19 (3859 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: GCC1 NM_024523.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

Genes affected

GCC1 (HGNC:19095): (GRIP and coiled-coil domain containing 1) The protein encoded by this gene is a peripheral membrane protein. It is sensitive to brefeldin A. This encoded protein contains a GRIP domain which is thought to be used in targeting. It may play a role in the organization of trans-Golgi network subcompartment involved with membrane transport. [provided by RefSeq, Jul 2008]

LOC105375490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GCC1	NM_024523.6	c.*1150A>G		3_prime_UTR_variant	2/2	ENST00000321407.3
LOC105375490	XR_007060511.1	n.91+8892A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GCC1	ENST00000321407.3	c.*1150A>G		3_prime_UTR_variant	2/2	1	NM_024523.6	P1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28435 AN: 152124 Hom.: 3855 Cov.: 33

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.190

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.187 AC: 28446 AN: 152242 Hom.: 3859 Cov.: 33 AF XY: 0.195 AC XY: 14524 AN XY: 74422

Gnomad4 AFR AF: 0.0441

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.193

Alfa AF: 0.200 Hom.: 3187

Bravo AF: 0.177

Asia WGS AF: 0.420 AC: 1456 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	3.2
DANN	Benign	0.54

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: rs989100; hg19: chr7-127220918;