6-41134344-G-A

Variant names:

• chr6-41134344-G-A
• rs6923053
• ENST00000567255.2:n.3638-841G>A

Variant summary

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

The ENST00000567255.2(ADCY10P1):​n.3638-841G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,120 control chromosomes in the GnomAD database, including 796 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 0.10 (796 hom., cov: 32)
• Consequence: ADCY10P1 ENST00000567255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 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.3638-841G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	ENST00000567255.2	TSL:1	n.3638-841G>A		intron	N/A
	ADCY10P1	ENST00000457653.8	TSL:6	n.2973-213G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15267 AN: 152002 Hom.: 797 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00598

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.100 AC: 15269 AN: 152120 Hom.: 796 Cov.: 32 AF XY: 0.0996 AC XY: 7410 AN XY: 74378

African (AFR) AF: 0.0906 AC: 3759 AN: 41504

American (AMR) AF: 0.110 AC: 1673 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3468

East Asian (EAS) AF: 0.00599 AC: 31 AN: 5176

South Asian (SAS) AF: 0.0894 AC: 431 AN: 4822

European-Finnish (FIN) AF: 0.0839 AC: 889 AN: 10594

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7601 AN: 67976

Other (OTH) AF: 0.109 AC: 230 AN: 2106

Alfa AF: 0.0678 Hom.: 74

Bravo AF: 0.103

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.67
PhyloP100		-0.40

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: rs6923053;

hg19: chr6-41102083;