rs6918289

Variant names:

• chr6-41134089-G-T
• rs6918289
• ENST00000567255.2:n.3638-1096G>T

Variant summary

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

The ENST00000567255.2(ADCY10P1):​n.3638-1096G>T 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 152,194 control chromosomes in the GnomAD database, including 739 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 (739 hom., cov: 32)
• Consequence: ADCY10P1 ENST00000567255.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 10 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=-0.87).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	NR_026938.2		n.3638-1096G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADCY10P1	ENST00000567255.2	TSL:1	n.3638-1096G>T		intron	N/A
	ADCY10P1	ENST00000457653.8	TSL:6	n.2973-468G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0962 AC: 14629 AN: 152076 Hom.: 740 Cov.: 32

Gnomad AFR AF: 0.0884

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.0840

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: 14637 AN: 152194 Hom.: 739 Cov.: 32 AF XY: 0.0941 AC XY: 7002 AN XY: 74404

African (AFR) AF: 0.0883 AC: 3664 AN: 41500

American (AMR) AF: 0.102 AC: 1565 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3468

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5190

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4822

European-Finnish (FIN) AF: 0.0840 AC: 891 AN: 10602

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

European-Non Finnish (NFE) AF: 0.110 AC: 7489 AN: 68012

Other (OTH) AF: 0.105 AC: 222 AN: 2110

Alfa AF: 0.105 Hom.: 463

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	-0.87
CADD	Benign	4.3
DANN	Benign	0.78
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6918289; hg19: chr6-41101828;