rs6905117

Positions:

• chr6-41122510-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026938.2(ADCY10P1):​n.2745-467T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,168 control chromosomes in the GnomAD database, including 790 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 (790 hom., cov: 32)
• Consequence: ADCY10P1 NR_026938.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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.2745-467T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADCY10P1	ENST00000457653.8	n.2122-467T>C		intron_variant, non_coding_transcript_variant
ADCY10P1	ENST00000567255.2	n.2745-467T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15208 AN: 152050 Hom.: 791 Cov.: 32

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0899

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: 15211 AN: 152168 Hom.: 790 Cov.: 32 AF XY: 0.0993 AC XY: 7389 AN XY: 74414

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00560

Gnomad4 SAS AF: 0.0892

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.109

Alfa AF: 0.111 Hom.: 465

Bravo AF: 0.102

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	-0.94
CADD	Benign	3.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6905117; hg19: chr6-41090249;