8-6878599-C-T

Variant names:

• chr8-6878599-C-T
• rs2978863
• ENST00000531701.2:n.602-6523C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531701.2(GS1-24F4.2):​n.602-6523C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,956 control chromosomes in the GnomAD database, including 5,852 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 0.27 (5852 hom., cov: 31)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 3 publications found

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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	ENST00000531701.2	n.602-6523C>T		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1	n.352-6523C>T		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1	n.794-6523C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41014 AN: 151838 Hom.: 5846 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.270 AC: 41040 AN: 151956 Hom.: 5852 Cov.: 31 AF XY: 0.267 AC XY: 19808 AN XY: 74268

African (AFR) AF: 0.199 AC: 8231 AN: 41456

American (AMR) AF: 0.291 AC: 4447 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2319 AN: 5148

South Asian (SAS) AF: 0.255 AC: 1224 AN: 4808

European-Finnish (FIN) AF: 0.189 AC: 1993 AN: 10546

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20707 AN: 67942

Other (OTH) AF: 0.307 AC: 645 AN: 2104

Alfa AF: 0.185 Hom.: 556

Bravo AF: 0.275

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.9
DANN	Benign	0.39
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs2978863; hg19: chr8-6736121;