6-10335252-T-C

Variant names:

• chr6-10335252-T-C
• rs17571811
• ENST00000756634.1:n.262-8775A>G

Variant summary

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

The ENST00000756634.1(ENSG00000298577):​n.262-8775A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,224 control chromosomes in the GnomAD database, including 2,902 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 0.17 (2902 hom., cov: 32)
• Consequence: ENSG00000298577 ENST00000756634.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 2 publications found

Genes affected

ENSG00000298577 (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 (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756634.1. 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
	ENSG00000298577	ENST00000756634.1		n.262-8775A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26042 AN: 152106 Hom.: 2905 Cov.: 32

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.171 AC: 26035 AN: 152224 Hom.: 2902 Cov.: 32 AF XY: 0.170 AC XY: 12628 AN XY: 74416

African (AFR) AF: 0.0521 AC: 2165 AN: 41564

American (AMR) AF: 0.145 AC: 2212 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3466

East Asian (EAS) AF: 0.0308 AC: 160 AN: 5188

South Asian (SAS) AF: 0.125 AC: 605 AN: 4824

European-Finnish (FIN) AF: 0.258 AC: 2728 AN: 10578

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16561 AN: 68010

Other (OTH) AF: 0.176 AC: 371 AN: 2110

Alfa AF: 0.210 Hom.: 3043

Bravo AF: 0.158

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17571811; hg19: chr6-10335485;