6-88133671-A-G

Variant names:

• chr6-88133671-A-G
• rs10485171
• ENST00000756364.1:n.128+8074A>G

Variant summary

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

The ENST00000756364.1(ENSG00000298549):​n.128+8074A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,986 control chromosomes in the GnomAD database, including 14,662 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 0.43 (14662 hom., cov: 33)
• Consequence: ENSG00000298549 ENST00000756364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 16 publications found

Genes affected

ENSG00000298549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756364.1. 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
	ENSG00000298549	ENST00000756364.1		n.128+8074A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65152 AN: 151868 Hom.: 14670 Cov.: 33

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.429 AC: 65162 AN: 151986 Hom.: 14662 Cov.: 33 AF XY: 0.426 AC XY: 31632 AN XY: 74282

African (AFR) AF: 0.466 AC: 19283 AN: 41420

American (AMR) AF: 0.308 AC: 4705 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.0847 AC: 438 AN: 5170

South Asian (SAS) AF: 0.348 AC: 1677 AN: 4822

European-Finnish (FIN) AF: 0.541 AC: 5715 AN: 10556

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31052 AN: 67966

Other (OTH) AF: 0.381 AC: 806 AN: 2116

Alfa AF: 0.432 Hom.: 59850

Bravo AF: 0.411

Asia WGS AF: 0.243 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	8.3
DANN	Benign	0.60
PhyloP100		-0.52

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: rs10485171;

hg19: chr6-88843390;

COSMIC: COSV69412238;