rs6923053

Positions:

• chr6-41134344-G-A
• chr6-41134344-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ADCY10P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCY10P1	NR_026938.2	n.3638-841G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADCY10P1	ENST00000567255.2	n.3638-841G>A		intron_variant		1
ADCY10P1	ENST00000457653.8	n.2973-213G>A		intron_variant		6

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

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00599

Gnomad4 SAS AF: 0.0894

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0665 Hom.: 71

Bravo AF: 0.103

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6923053; hg19: chr6-41102083;