ENST00000567255.2:n.3017+319C>A

Variant names:

• chr6-41123568-C-A
• rs11969526
• ENST00000567255.2:n.3017+319C>A

Variant summary

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

The ENST00000567255.2(ADCY10P1):​n.3017+319C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 152,214 control chromosomes in the GnomAD database, including 744 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 0.096 (744 hom., cov: 32)
• Consequence: ADCY10P1 ENST00000567255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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.3017+319C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	ENST00000567255.2	TSL:1	n.3017+319C>A		intron	N/A
	ADCY10P1	ENST00000457653.8	TSL:6	n.2394+319C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0962 AC: 14635 AN: 152096 Hom.: 745 Cov.: 32

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0962 AC: 14644 AN: 152214 Hom.: 744 Cov.: 32 AF XY: 0.0941 AC XY: 7006 AN XY: 74420

African (AFR) AF: 0.0884 AC: 3672 AN: 41522

American (AMR) AF: 0.103 AC: 1569 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5180

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4824

European-Finnish (FIN) AF: 0.0839 AC: 889 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7490 AN: 68006

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.103 Hom.: 1323

Bravo AF: 0.0995

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.29
PhyloP100		-0.59

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: rs11969526;

hg19: chr6-41091307;