6-41115768-A-G

Variant names:

• chr6-41115768-A-G
• rs6926018
• ENST00000567255.2:n.1585-1530A>G

Variant summary

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

The ENST00000567255.2(ADCY10P1):​n.1585-1530A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.966 in 152,322 control chromosomes in the GnomAD database, including 71,095 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 0.97 (71095 hom., cov: 31)
• Consequence: ADCY10P1 ENST00000567255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 4 publications found

Genes affected

ADCY10P1 (HGNC:):

ADCY10P1 (HGNC:44143): (ADCY10 pseudogene 1)

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 (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567255.2. 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
	ADCY10P1	NR_026938.2		n.1585-1530A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	ENST00000567255.2	TSL:1	n.1585-1530A>G		intron	N/A
	ADCY10P1	ENST00000457653.8	TSL:6	n.1005-1530A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.966 AC: 147020 AN: 152204 Hom.: 71037 Cov.: 31

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.966 AC: 147138 AN: 152322 Hom.: 71095 Cov.: 31 AF XY: 0.965 AC XY: 71880 AN XY: 74468

African (AFR) AF: 0.982 AC: 40812 AN: 41564

American (AMR) AF: 0.980 AC: 14998 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.964 AC: 3344 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5186 AN: 5188

South Asian (SAS) AF: 0.988 AC: 4765 AN: 4822

European-Finnish (FIN) AF: 0.915 AC: 9709 AN: 10610

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65079 AN: 68040

Other (OTH) AF: 0.973 AC: 2055 AN: 2112

Alfa AF: 0.960 Hom.: 49382

Bravo AF: 0.972

Asia WGS AF: 0.995 AC: 3461 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	4.6
DANN	Benign	0.68
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs6926018; hg19: chr6-41083507;