8-6878545-G-C

Position:

• chr8-6878545-G-C

Variant summary

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

The ENST00000531701.1(GS1-24F4.2):​n.226-6577G>C 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 0.721 in 151,968 control chromosomes in the GnomAD database, including 39,599 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 0.72 (39599 hom., cov: 32)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-6577G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109431 AN: 151850 Hom.: 39589 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.721 AC: 109493 AN: 151968 Hom.: 39599 Cov.: 32 AF XY: 0.724 AC XY: 53761 AN XY: 74262

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.742

Alfa AF: 0.721 Hom.: 4910

Bravo AF: 0.713

Asia WGS AF: 0.769 AC: 2676 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	0.36
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2702877; hg19: chr8-6736067;