6-41115613-G-A

Variant names:

• chr6-41115613-G-A
• rs10456499
• ENST00000567255.2:n.1585-1685G>A

Variant summary

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

The ENST00000567255.2(ADCY10P1):​n.1585-1685G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 152,022 control chromosomes in the GnomAD database, including 38,015 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 0.69 (38015 hom., cov: 30)
• Consequence: ADCY10P1 ENST00000567255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 14 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	NR_026938.2		n.1585-1685G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	ENST00000567255.2	TSL:1	n.1585-1685G>A		intron	N/A
	ADCY10P1	ENST00000457653.8	TSL:6	n.1005-1685G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105191 AN: 151904 Hom.: 37953 Cov.: 30

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.693 AC: 105313 AN: 152022 Hom.: 38015 Cov.: 30 AF XY: 0.691 AC XY: 51290 AN XY: 74276

African (AFR) AF: 0.907 AC: 37644 AN: 41506

American (AMR) AF: 0.639 AC: 9760 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2112 AN: 3466

East Asian (EAS) AF: 0.765 AC: 3934 AN: 5144

South Asian (SAS) AF: 0.713 AC: 3428 AN: 4808

European-Finnish (FIN) AF: 0.567 AC: 5991 AN: 10560

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.592 AC: 40226 AN: 67960

Other (OTH) AF: 0.673 AC: 1421 AN: 2110

Alfa AF: 0.613 Hom.: 56571

Bravo AF: 0.707

Asia WGS AF: 0.788 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.96
DANN	Benign	0.31
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs10456499; hg19: chr6-41083352;