6-108532290-A-G

Variant names:

• chr6-108532290-A-G
• rs17041
• ENST00000659932.2:n.136+25874T>C

Variant summary

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

The ENST00000659932.2(ENSG00000287044):​n.136+25874T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,984 control chromosomes in the GnomAD database, including 15,732 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 (15732 hom., cov: 32)
• Consequence: ENSG00000287044 ENST00000659932.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 5 publications found

Genes affected

ENSG00000287044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659932.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287044	ENST00000659932.2		n.136+25874T>C		intron	N/A
	ENSG00000287044	ENST00000784390.1		n.119+25874T>C		intron	N/A
	ENSG00000287044	ENST00000784391.1		n.126+25874T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68980 AN: 151866 Hom.: 15729 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.454 AC: 69024 AN: 151984 Hom.: 15732 Cov.: 32 AF XY: 0.450 AC XY: 33422 AN XY: 74258

African (AFR) AF: 0.430 AC: 17835 AN: 41450

American (AMR) AF: 0.467 AC: 7130 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1402 AN: 5160

South Asian (SAS) AF: 0.420 AC: 2024 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5017 AN: 10550

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32480 AN: 67958

Other (OTH) AF: 0.468 AC: 988 AN: 2110

Alfa AF: 0.472 Hom.: 48643

Bravo AF: 0.457

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs17041; hg19: chr6-108853493;