rs10484842

Variant names:

• chr6-46895523-C-A
• rs10484842
• NM_001098518.2:c.157+4506G>T

Variant summary

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

The NM_001098518.2(ADGRF5):​c.157+4506G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 151,146 control chromosomes in the GnomAD database, including 895 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 0.078 (895 hom., cov: 31)
• Consequence: ADGRF5 NM_001098518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 1 publications found

Genes affected

ADGRF5 (HGNC:19030): (adhesion G protein-coupled receptor F5) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway and cell surface receptor signaling pathway. Predicted to act upstream of or within several processes, including glomerular filtration; pharyngeal arch artery morphogenesis; and surfactant homeostasis. Located in cell surface and cytoplasmic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADGRF5	NM_001098518.2	c.157+4506G>T		intron_variant	Intron 3 of 20	ENST00000283296.12	NP_001091988.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADGRF5	ENST00000283296.12	c.157+4506G>T		intron_variant	Intron 3 of 20	1	NM_001098518.2	ENSP00000283296.7
ADGRF5	ENST00000265417.7	c.157+4506G>T		intron_variant	Intron 3 of 20	1		ENSP00000265417.6

Frequencies

GnomAD3 genomes AF: 0.0781 AC: 11788 AN: 151024 Hom.: 893 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0441

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.0497

Gnomad EAS AF: 0.00334

Gnomad SAS AF: 0.0303

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.0673

Gnomad NFE AF: 0.0296

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0781 AC: 11808 AN: 151146 Hom.: 895 Cov.: 31 AF XY: 0.0761 AC XY: 5618 AN XY: 73798

African (AFR) AF: 0.200 AC: 8208 AN: 41078

American (AMR) AF: 0.0511 AC: 775 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.0497 AC: 172 AN: 3462

East Asian (EAS) AF: 0.00335 AC: 17 AN: 5080

South Asian (SAS) AF: 0.0306 AC: 143 AN: 4678

European-Finnish (FIN) AF: 0.0260 AC: 274 AN: 10542

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0296 AC: 2011 AN: 67868

Other (OTH) AF: 0.0712 AC: 148 AN: 2080

Alfa AF: 0.0761 Hom.: 148

Bravo AF: 0.0874

Asia WGS AF: 0.0320 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.75
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10484842; hg19: chr6-46863260;