8-6880122-C-T

Variant names:

• chr8-6880122-C-T
• rs2978862
• ENST00000531701.1:n.226-5000C>T

Variant summary

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

The ENST00000531701.1(GS1-24F4.2):​n.226-5000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,114 control chromosomes in the GnomAD database, including 2,815 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 0.17 (2815 hom., cov: 33)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-5000C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25247 AN: 151996 Hom.: 2809 Cov.: 33

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.166 AC: 25253 AN: 152114 Hom.: 2815 Cov.: 33 AF XY: 0.174 AC XY: 12975 AN XY: 74356

Gnomad4 AFR AF: 0.0383

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.142

Alfa AF: 0.114 Hom.: 240

Bravo AF: 0.152

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2978862; hg19: chr8-6737644;