8-6857177-A-G

Variant names:

• chr8-6857177-A-G
• rs11777699
• ENST00000531701.2:n.601+12248A>G

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.601+12248A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,028 control chromosomes in the GnomAD database, including 16,250 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 0.45 (16250 hom., cov: 33)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.552 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.601+12248A>G		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000655804.2	n.340-16004A>G		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000657010.1	n.790+12248A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68861 AN: 151910 Hom.: 16250 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.453 AC: 68873 AN: 152028 Hom.: 16250 Cov.: 33 AF XY: 0.457 AC XY: 33944 AN XY: 74330

African (AFR) AF: 0.335 AC: 13894 AN: 41442

American (AMR) AF: 0.514 AC: 7858 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1681 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1376 AN: 5174

South Asian (SAS) AF: 0.570 AC: 2746 AN: 4816

European-Finnish (FIN) AF: 0.541 AC: 5718 AN: 10570

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33928 AN: 67972

Other (OTH) AF: 0.488 AC: 1029 AN: 2108

Alfa AF: 0.483 Hom.: 80230

Bravo AF: 0.443

Asia WGS AF: 0.419 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.18
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11777699; hg19: chr8-6714699;