rs989100

Variant names:

• chr7-127580864-T-C
• rs989100
• NM_024523.6:c.*1150A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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]

ENSG00000295686 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GCC1	NM_024523.6	c.*1150A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000321407.3	NP_078799.2
LOC105375490	XR_007060511.1	n.91+8892A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCC1	ENST00000321407.3	c.*1150A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_024523.6	ENSP00000318821.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0441 AC: 1836 AN: 41586

American (AMR) AF: 0.218 AC: 3334 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.685 AC: 3538 AN: 5166

South Asian (SAS) AF: 0.264 AC: 1273 AN: 4830

European-Finnish (FIN) AF: 0.280 AC: 2965 AN: 10586

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14438 AN: 68000

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.194 Hom.: 3989

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
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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: rs989100; hg19: chr7-127220918;