8-6878467-C-T

Variant names:

• chr8-6878467-C-T
• rs2741132
• ENST00000531701.2:n.602-6655C>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.602-6655C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,862 control chromosomes in the GnomAD database, including 6,814 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 0.29 (6814 hom., cov: 31)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531701.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-6655C>T		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-6655C>T		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-6655C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44189 AN: 151744 Hom.: 6808 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.291 AC: 44214 AN: 151862 Hom.: 6814 Cov.: 31 AF XY: 0.288 AC XY: 21363 AN XY: 74210

African (AFR) AF: 0.220 AC: 9107 AN: 41416

American (AMR) AF: 0.307 AC: 4681 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3466

East Asian (EAS) AF: 0.452 AC: 2310 AN: 5114

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4812

European-Finnish (FIN) AF: 0.191 AC: 2009 AN: 10538

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21956 AN: 67940

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.239 Hom.: 987

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.52
PhyloP100		-3.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2741132;

hg19: chr8-6735989;