7-7968245-G-A

Position:

• chr7-7968245-G-A

Variant summary

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

The NR_110018.1(GLCCI1-DT):​n.209+299C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,128 control chromosomes in the GnomAD database, including 30,608 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 0.63 (30608 hom., cov: 33)
• Consequence: GLCCI1-DT NR_110018.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

Genes affected

GLCCI1-DT (HGNC:40852): (GLCCI1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLCCI1-DT	NR_110018.1	n.209+299C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLCCI1-DT	ENST00000428660.1	n.132+1527C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95411 AN: 152010 Hom.: 30581 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.628 AC: 95480 AN: 152128 Hom.: 30608 Cov.: 33 AF XY: 0.623 AC XY: 46354 AN XY: 74354

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.647

Alfa AF: 0.575 Hom.: 24460

Bravo AF: 0.640

Asia WGS AF: 0.492 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.4
DANN	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs37973; hg19: chr7-8007876;